Optics, devices, and systems for assays

Abstract

Furthermore, the present application provides devices and methods for simple, rapid and sensitive assays.

Description

[0001] This application is a divisional application filed with respect to the Chinese national phase application with application number 2018800209738 and application date of 2018-02-08.

[0002] Cross-citation of related applications

[0003] This application claims priority to U.S. Provisional Patent Application No. 62 / 456,590, filed February 8, 2017; Serial No. 62 / 459,554, filed February 15, 2017; Serial No. 62 / 460,075, filed February 16, 2017; Serial No. 62 / 456,504 (ESX045PRV), filed February 8, 2017; Serial No. 62 / 460,062 (ESX045PRV2), filed February 16, 2017; and Serial No. 62 / 457,133 (ESX046PRV), filed February 9, 2017, the entire contents of which are incorporated herein by reference for all purposes. Technical Field

[0004] This invention relates to apparatus and methods for performing biological and chemical measurements and computational imaging. Background Technology

[0005] In biological and chemical assays (e.g., diagnostic tests), simple, rapid, and sensitive assays (including imaging) are often required. This invention particularly provides apparatus and methods for simple, rapid, and sensitive assays (including imaging). Attached Figure Description

[0006] Those skilled in the art will understand that the accompanying drawings described below are for illustrative purposes only. The drawings are not intended to limit the scope of the invention in any way. The drawings are not drawn to scale. In the graphs showing experimental data points, the lines connecting the data points are only for guiding observation and have no other meaning.

[0007] Figure 1A , 1B 1C is a schematic diagram of a system test sample under fluorescent illumination mode according to some embodiments of the present invention.

[0008] Figure 2A , 2B Figures 2 and 2C are schematic diagrams of system test samples under bright field illumination mode according to some embodiments of the present invention.

[0009] Figure 3 This is a schematic exploded view of the system and the optical adapter device in system 20 according to some embodiments of the present invention.

[0010] Figure 4 This is a schematic cross-sectional view showing details of a system test sample, particularly the apparatus, in a bright field illumination mode according to some embodiments of the present invention.

[0011] Figure 5 This is a schematic cross-sectional view showing details of a system test sample, particularly the apparatus, under fluorescent illumination mode according to some embodiments of the present invention.

[0012] Figure 6A and Figure 6B This is a schematic cross-sectional view illustrating a design according to some embodiments of the invention to stop the lever at a predetermined position when pulled outward from the device.

[0013] Figure 7 This is a schematic diagram of the structure of the sample slider of the QMAX device according to some embodiments of the present invention.

[0014] Figure 8 This is a schematic diagram of a movable arm that switches between two predetermined stop positions according to some embodiments of the present invention.

[0015] Figure 9 This is a schematic diagram illustrating how a slider, according to some embodiments of the present invention, indicates whether a QMAX device is inserted in the correct direction.

[0016] Figure 10A , 10B 10C is a schematic diagram of a system for a smartphone colorimeter reader according to some embodiments of the present invention.

[0017] Figure 11 This is a schematic exploded view of an optical adapter device in a system according to some embodiments of the present invention.

[0018] Figure 12 This is a schematic cross-sectional view showing details of a system for reading color charts according to some embodiments of the invention, particularly details of the apparatus.

[0019] Figure 13A , 13B Figures 1 and 13C are schematic diagrams of a system for a smartphone colorimeter reader according to some embodiments of the present invention.

[0020] Figure 14 This is a schematic exploded view of an optical adapter device in a system according to some embodiments of the present invention.

[0021] Figure 15A , 15B Figures 1 and 15C are schematic diagrams illustrating details of a system for reading color charts, particularly an apparatus, according to some embodiments of the present invention.

[0022] Figure 16A A tomographic apparatus comprising an imaging sensor, a lens, and a QMAX structure, according to some embodiments of the present invention, is shown.

[0023] Figure 16B An example of a column array pattern of the letter E is shown.

[0024] Figure 16C A thin lens model is shown, which explains the effect of focal length on the captured image.

[0025] Figure 16D The image was captured by the imaging sensor. Figure 16B An image of an exemplary column array.

[0026] Figure 16E A diagram of a scheme based on phase image retrieval is shown.

[0027] Figure 17A An analyte detection and localization workflow comprising two phases, training, and prediction, is illustrated according to some embodiments of the invention.

[0028] Figure 17B The process of removing an item from a sorting list is illustrated according to some embodiments of the present invention.

[0029] Figure 18 An implementation scheme of the QMAX device for cell imaging is shown.

[0030] Figure 19A A schematic diagram of a dual-camera imaging system is shown.

[0031] Figure 19B A schematic diagram illustrating the distance selection between the two cameras is shown.

[0032] Figure 19C The results of the dual-camera images are shown for comparison.

[0033] Detailed description of exemplary implementation schemes

[0034] The following detailed description illustrates some embodiments of the invention by way of example, not limitation. Section headings and any subheadings used herein are for organizational purposes only and should not be construed as limiting the subject matter in any way. The content under section headings and / or subheadings is not limited to the section headings and / or subheadings, but applies to the entire description of the invention.

[0035] References to any publication are for information prior to the filing date and should not be construed as an admission that this claim is not entitled to a prior invention prior to such publication. Furthermore, the provided publication date may differ from the actual publication date, which may require independent verification.

[0036] Seven exemplary embodiments are shown below: one embodiment of an optical adapter for bright-field and fluorescence microscopy attached to a smartphone; one embodiment of an optical adapter for colorimetry measurement attached to a smartphone using a tilted fiber end face as a light source; one embodiment of an optical adapter for colorimetry measurement attached to a smartphone using side illumination from a loop fiber as a light source; one embodiment of a tomographic imaging apparatus and method; one embodiment of machine learning-assisted analysis and imaging; one embodiment of an apparatus and method for tissue staining and cell imaging; and one embodiment of a dual-lens imaging system.

[0037] A. Optical adapter for attaching bright-field and fluorescence microscopes to smartphones.

[0038] Bright-field and fluorescence microscopy are powerful techniques for examining certain properties of samples, with wide applications in health monitoring, disease diagnosis, and science education. However, traditionally, capturing microscopic images requires expensive microscopes and experienced personnel, making it inaccessible to the average person. Although some recently invented accessories can turn smartphones into bright-field microscopes, such bright-field microscopy images provide only very limited information about the sample.

[0039] The invention described herein addresses this problem by providing a system comprising an optical adapter and a smartphone. The optical adapter is mounted on the smartphone, converting it into a microscope capable of capturing fluorescence and bright-field images of samples. The system can be conveniently and reliably operated by ordinary personnel in any location. Utilizing existing resources of the smartphone, including the camera, light source, processor, and display, the optical adapter provides the user with a low-cost solution for bright-field and fluorescence microscopy.

[0040] In this invention, the optical adapter includes a retainer frame that fits onto the upper part of the mobile phone and an optical box attached to the retainer, which has a sample receiver slot and illumination optics. In some prior art (US Patent Nos. 2004 / 029091 and 2011 / 0292198), their optical adapter designs are integral pieces comprising clip-on mechanical components and functional optical elements mounted on the smartphone. The problem with this design is that it requires redesigning the entire optical adapter for each specific smartphone model. However, in this invention, the optical adapter is divided into a retainer frame solely for assembling the smartphone and a universal optical box containing all functional components. For smartphones of different sizes, as long as the relative positions of the camera and light source are the same, only the mounting bracket needs to be redesigned, saving significant design and manufacturing costs.

[0041] The optical adapter's optical housing includes: a receiver slot that receives the sample within the field of view and focal length of the smartphone camera and positions the sample in a sample slide; a bright-field illumination optics for capturing a bright-field microscopic image of the sample; a fluorescent illumination optics for capturing a fluorescent microscopic image of the sample; and a lever that switches between the bright-field illumination optics and the fluorescent illumination optics by sliding inward and outward within the optical housing.

[0042] The receiver slot has a rubber door attached thereto, which completely covers the slot to prevent ambient light from entering the optical chamber and being collected by the camera. In the prior art (US Patent 2016 / 0290916), the sample slot is always exposed to ambient light, which does not cause much of a problem since it is only used for bright-field microscopy. However, this invention can utilize this rubber door when performing fluorescence microscopy, because ambient light introduces a lot of noise into the camera's image sensor.

[0043] To capture good fluorescence microscopy images, it is desirable for almost no excitation light to enter the camera, and for the camera to collect only the fluorescence emitted by the sample. However, for all ordinary smartphones, due to the large divergence angle of the light beam emitted from the light source, optical filters placed in front of the camera are not good at blocking unwanted wavelength ranges of light emitted from the smartphone's light source, and optical filters are ineffective for uncollimated beams. Collimating optics can be designed to collimate the light emitted from the smartphone's light source to solve this problem, but this approach increases the size and cost of the adapter. In contrast, in this invention, the fluorescence illumination optics allow the excitation light to illuminate the sample partially from a waveguide inside the sample slide and partially from the rear side of the sample side at a large oblique angle of incidence, so that the excitation light is almost not collected by the camera, thus reducing the noise signal entering the camera.

[0044] The bright-field illumination optics in the adapter receive and rotate the beam of light emitted by the light source so as to backlight the sample at a vertical angle of incidence.

[0045] Typically, the optical box also includes a lens mounted therein, aligned with the smartphone's camera, which magnifies the image captured by the camera. The image captured by the camera can be further processed by the smartphone's processor, and the analysis results can be output to the smartphone's screen.

[0046] To implement both bright-field and fluorescent illumination optics within the same optical adapter, a sliding lever is used in this invention. The optical element of the fluorescent illumination optics is mounted on the lever, and when the lever is fully inserted into the optical housing, the fluorescent illumination optics block the light path of the bright-field illumination optics and switch the illumination optics to the fluorescent illumination optics. When the lever is slid out, the fluorescent illumination optics mounted on the lever move out of the light path and switch back to the bright-field illumination optics. This lever design allows the optical adapter to operate in both bright-field and fluorescent illumination modes without requiring two separate single-mode optical housings.

[0047] A lever consists of two planes at different heights and on different planes.

[0048] In some implementations, the two planes can be connected together using a vertical bar and moved into or out of the optical box together. In other implementations, the two planes can be separated, and each plane can be moved into or out of the optical box individually.

[0049] The upper lever plane includes at least one optical element, which may be, but is not limited to, a filter. The upper lever plane moves below the light source, and the preferred distance between the upper lever plane and the light source is in the range of 0 to 5 mm.

[0050] A portion of the bottom lever plane is not parallel to the image plane. The non-parallel portion of the bottom lever plane has a highly specular surface finish with a reflectivity greater than 95%. This non-parallel portion of the bottom lever plane moves below the light source and deflects the light emitted from the source to illuminate the sample area directly below the camera. The preferred tilt angle of the non-parallel portion of the bottom lever plane is in the range of 45 to 65 degrees, and the tilt angle is defined as the angle between the non-parallel bottom plane and the vertical plane.

[0051] A portion of the bottom lever plane is parallel to the image plane and located 1 mm to 10 mm below the sample. The surface of the parallel portion of the bottom lever plane is highly light-absorbing, with light absorption greater than 95%. This absorbing surface is used to eliminate reflected light back-illuminated onto the sample at a small incident angle.

[0052] To allow the lever to slide in and out to switch the illumination optics, a stop design including a ball stop and a groove on the lever is used to stop the lever in a predetermined position when pulled outward from the adapter. This allows the user to pull the lever with any force, but to stop it in a fixed position where the optical adapter's operating mode is switched to brightfield illumination.

[0053] The sample slider is installed in the receiver slot to receive the QMAX device and position the sample within the QMAX device, which is within the field of view and focus of the smartphone camera.

[0054] The sample slider includes a fixed track frame and a movable arm:

[0055] The frame track is fixedly mounted in the receiver slot of the optical box. The track frame has slide grooves that match the width and thickness of the QMAX device, allowing the QMAX device to slide along the track. The width and height of the track grooves are carefully configured such that the QMAX device moves less than 0.5 mm in the direction perpendicular to the sliding plane and less than 0.2 mm along the thickness direction of the QMAX device.

[0056] The frame track has an open window in the field of view of the phone's camera to allow light to reflect back onto the sample.

[0057] The movable arm is pre-set in the slide rail groove of the track frame and moves together with the QMAX device to guide the movement of the QMAX device in the track frame.

[0058] The movable arm is equipped with a stop mechanism having two predetermined stopping positions. In one position, the arm will stop the QMAX device at a location where the fixed sampling area on the QMAX device is exactly below the smartphone's camera. In the other position, the arm will stop the QMAX device at a location where the sampling area on the QMAX device is outside the smartphone's field of view, and the QMAX device can be easily removed from the track slot.

[0059] By pressing the QMAX device and the movable arm together to the end of the track groove and then releasing, the movable arm switches between two stop positions.

[0060] The movable arm indicates whether the QMAX device is inserted in the correct direction. One corner of the QMAX device is configured to have a different shape from the other three right angles. The shape of the movable arm matches the specific shape of this corner, ensuring that the QMAX device can only slide into the correct position in the track groove in the correct direction.

[0061] Figure 1A , 1B Figure 1C is a schematic diagram of system 19 used to test samples under fluorescence illumination mode. Specifically, Figure 1B and 1C These are exploded views of system 19 shown from the front and rear sides, respectively. System 19 includes a smartphone 1; an optical adapter device 18 mounted on the upper part of the smartphone 1; and a sample slide 5 inserted into the receiver slot 4 of device 18, such that the sample on the sample slide 5 is within the field of view and focus of the camera module 1C in the smartphone 1. A lever 8 is fully pressed into device 18, causing system 19 to operate in fluorescence illumination mode. After the sample slide 5 is inserted, a rubber door 16 connected to device 18 covers the receiver slot 4 to prevent ambient light from entering the receiver slot 4 and affecting the test.

[0062] The software (not shown) installed in the smartphone 1 analyzes the image collected by the camera module 1C while the light source 1L in the smartphone 1 is emitting light, so as to obtain some properties of the sample, and outputs the results to the display screen 1f in the smartphone 1.

[0063] Figure 2A , 2B Figure 2C is a schematic diagram of system 20 used to test samples under bright field illumination mode. Specifically, Figure 2B and 2C These are exploded views of system 20, shown from the front and rear sides, respectively. System 20 includes a smartphone 1; an optical adapter device 18 mounted on the upper part of the smartphone 1; and a sample carrier 5 inserted into the receiver slot 4 of device 18 such that the sample on the sample carrier 5 is within the field of view and focus of the camera module 1C in the smartphone 1. A lever 8 is pulled outward from device 18 and stopped by a brake (not shown) at a predetermined position in device 18, causing system 20 to operate in bright field illumination mode.

[0064] Figure 3 This is a schematic exploded view of the optical adapter device 18 in systems 19 and 20. Device 18 includes a bracket housing 2 mounted on the upper part of the smartphone 1; an optical box 3 attached to the housing 2, including a receiver slot 4, an optical chamber 3C, tracks 6b and 6t allowing a lever 8 to slide into, and a rubber door 16 inserted into a groove 4s to cover the receiver slot 4. An optical insert 7 is fitted to the top of the optical chamber 3C, wherein the exit aperture 7L and the inlet aperture 7C are aligned with the light source 1L and camera 1C in the smartphone 1 (e.g., ...). Figure 2B (As shown). Lens 11 is mounted in the inlet aperture 7C of optical insert 7 and configured such that the sample in the sample carrier 5 inserted into the receiver slot 4 is within the working distance of camera 1C (e.g., Figure 2B and 1B (As shown). Lens 11 is used to magnify the image produced by camera 1C (e.g., ...). Figure 2B and 1B(As shown) The image of the captured sample. A long-pass optical filter 12 is mounted in the inlet aperture 7C at the top of the lens 11. A pair of right-angle mirrors 13 and 14 are mounted on the bottom of the optical chamber 3C and are configured such that mirrors 13 and 14 are aligned with the light source 1L and the camera 1C respectively (as shown). Figure 2B and 1B (As shown). In the following Figure 4 The mirrors 13 and 14 are described in the same manner as the bright-field illumination optics in device 18. Lever 8 includes two horizontal bars: the upper horizontal bar includes a bandpass filter 15 mounted in slot 8a, while the lower horizontal bar includes a light absorber 9 mounted on a horizontal plane 8b and a mirror 10 mounted on an inclined plane 8c. Below... Figure 5 The filter 15, light absorber 9, and reflector 10 operate in the same manner as the fluorescent illumination optics in device 18. The upper horizontal bar of lever 8 slides along track 6t within box 3, while the lower horizontal bars 8b and 8c slide along track 6b within box 3. Lever 8 stops at two different positions within box 3 to switch between bright-field illumination optics and fluorescent illumination optics. Lever 8 is fully inserted into box 3 to switch device 18 to operate with fluorescent illumination optics. Ball stopper 17 is mounted on the side wall of track 6t so that when lever 8 is pulled outward from box 3 to switch device 18 to operate with bright-field illumination optics, lever 8 stops at a predetermined position.

[0065] Figure 4 This is a schematic cross-sectional view showing details of the system 20 for testing samples under bright field illumination, particularly details of the apparatus 18. This figure illustrates the above references. Figure 3 The function of the described component. Pulling lever 8 outward from device 18 (e.g.) Figure 3 (as shown) and stopped by stop 17 (as shown) Figure 3 (As shown) At a predetermined position, reflectors 13 and 14 are exposed to and aligned with camera 1C and light source 1L. Light source 1L emits beam BB1 away from smartphone 1. Beam BB1 is deflected 90 degrees by reflector 14 to beam BB2, which is further deflected 90 degrees by reflector 13 to beam BB3. Beam BB3 illuminates the sample in sample slide 5 at a perpendicular angle of incidence. Lens 11 produces a magnified image of the sample on the image sensor plane of camera 1C. Smartphone 1 captures and processes the image to obtain certain properties of the sample.

[0066] Figure 5 This is a schematic cross-sectional view showing details of the system 19 for testing samples under fluorescence illumination mode, particularly details of the apparatus 18. This figure illustrates the above references. Figure 3 The function of the described component. Lever 8 (e.g.) Figure 3The light absorber 9 and the tilting mirror 10 are fully inserted into the device 18, such that the light absorber 9 and the tilting mirror 10 are within the field of view of the camera 1C and the light source 1L, and block the optical path between the light source 1L and the mirror pair 13 and 14. A bandpass filter 15 is located directly below the light source 1L. The light source 1L emits a beam BF1 away from the smartphone 1. The filter 15 allows the beam BF1, which has a specific wavelength range matching the excitation wavelength of the fluorescent sample in the sample slide 5, to pass through. A portion of the beam BF1 illuminates the edge of the transparent sample slide 5 and is coupled to a waveguide beam BF3 traveling in the sample slide 5, illuminating the sample area below the lens 11. A portion of the beam BF1 illuminates the mirror 10. The tilting mirror 10 deflects the beam BF1 to the beam BF2 and illuminates the sample area in the sample slide 5 directly below the lens 11 at a large tilt angle. The remaining portion of the beam BF1 with a large divergence angle (i.e., beam BF4) illuminates and is absorbed by absorber 9, preventing the reflected light from beam BF4 from entering camera 1C at a small angle of incidence. Light from the sample area below lens 11 passes through lens 11 and is filtered by long-pass filter 12, ensuring that only light within a specific wavelength range emitted by the fluorescent sample in sample slide 5 enters camera 1C to form an image. Smartphone 1 captures and processes the image to obtain certain properties of the sample. Rubber door 16 is inserted into device 18 to cover sample slide 5, preventing ambient light from entering device 18 and affecting the test.

[0067] Figure 6A and Figure 6B This is a schematic cross-sectional view showing the design that stops lever 8 at a predetermined position when it is pulled outward from device 18. A ball plug 17 is mounted in the sidewall of the track groove 6t, and a groove 8g is drilled in the sidewall of lever 8, the shape of which matches the shape of the ball in ball plug 17. When lever 8 is pulled outward from device 18 and has not yet reached the predetermined position shown in Figure 2, as... Figure 6A As shown, the ball in the ball plug 17 is pressed into the body of the lever 8 by the side wall of the lever 8, so that the lever 8 can slide along the track 6t. Figure 6B As shown, when the groove 8g on the lever 8 reaches the position of the ball plug 17, the ball in the ball plug 17 jumps into the groove 8g to stop the lever 8.

[0068] Figure 7This is a schematic diagram of the structure holding the sample slider of the QMAX device. The sample slider includes: a track frame having track grooves along which the QMAX device slides; and a movable arm, pre-positioned in the track grooves, moving with the QMAX device to guide its movement. The movable arm is equipped with a stop mechanism to stop the QMAX device at two predetermined stop positions. The width and height of the track grooves are carefully constructed such that the QMAX device moves less than 0.5 mm in the direction perpendicular to the sliding plane and less than 0.2 mm along the thickness direction of the QMAX device.

[0069] Figure 8 This is a schematic diagram of the movable arm switching between two predetermined stop positions. By pressing the QMAX device and the movable arm together to the end of the track groove and then releasing, the QMAX card can stop at position 1 or position 2. In position 1, the sample area is outside the field of view of the smartphone camera used to easily remove the QMAX device from the slider. In position 2, the sample area is exactly under the field of view of the smartphone camera used to capture images.

[0070] Figure 9 This is a schematic diagram illustrating how the slider indicates whether the QMAX device is inserted in the correct direction. One corner of the QMAX device is shaped differently from the other three right angles. The boom shape matches the corner shape of this specific configuration, ensuring the QMAX device can only slide into the correct position in the track slot in the correct direction. If the QMAX device is flipped or inserted from the wrong side, the portion of the QMAX device outside the slider is longer than when correctly inserted.

[0071] When both fluorescence and bright-field images are available, knowledge of the fluorescence image can be used to process the bright-field image, or vice versa, or both images can be processed together. The fields of view of the fluorescence and bright-field images can be different; therefore, the two images are not spatially aligned pixel-to-pixel.

[0072] To resolve misalignment between fluorescence and bright-field images, image registration can be applied to both images. Image registration finds a geometric transformation that correlates the spatial locations from one image to another. Various image registration algorithms can be used to align fluorescence and bright-field images, including but not limited to feature-point based, cross-correlation based, and Fourier-based alignment. The image registration output is a geometric transformation that maps the spatial locations (coordinates) of one image to those of the other.

[0073] After the fluorescence image and the bright field image are aligned, information from the two images can be used to improve the processing of one image, or to process the two images together. Example:

[0074] A1. An optical adapter, comprising:

[0075] i. Support frame, and

[0076] ii. An optical box that can be removably attached to a bracket frame.

[0077] The bracket frame is configured for removable mounting on a mobile device and aligning the optical box with the camera and lighting source integrated into the mobile device;

[0078] The optical box contains a sample receiver slot and illumination optics.

[0079] B1. An optical system comprising:

[0080] i. The optical adapter of implementation scheme A1; and

[0081] ii. A QMAX card comprising a first plate and a second plate, wherein the first and second plates compress a liquid sample into a uniform thickness layer of less than 200 μm; and

[0082] iii. A slider configured to receive a QMAX card and be inserted into the optical cartridge.

[0083] C1. The adapter or system according to any of the foregoing embodiments, wherein the mobile device is a smartphone.

[0084] C2. The adapter or system according to any of the foregoing embodiments, wherein the retainer frame includes a retainer housing configured to be replaceable with other retainer housings of different sizes for different mobile devices.

[0085] C3. The adapter or system according to any of the foregoing embodiments, wherein the size of the retainer frame is adapted to removably mount the optical adapter to the upper part of the mobile device.

[0086] C4. The adapter or system according to any of the foregoing embodiments, wherein the optical adapter's optical housing comprises:

[0087] i. Receiver slot, which is configured to receive and position the QMAX card in the sample carrier within the camera's field of view and focal range;

[0088] ii. Bright-field illumination optics configured to capture bright-field microscopic images of a sample;

[0089] iii. A fluorescence illumination optics configured to capture a fluorescence microscopic image of a sample; and

[0090] iv. A lever configured to switch between bright-field illumination optics and fluorescent illumination optics by sliding inward and outward within the optical box.

[0091] C5. The adapter or system according to any of the foregoing embodiments, wherein the receiver slot includes a rubber door that can completely cover the slot to prevent ambient light from entering the light box for collection by the camera.

[0092] C6. The adapter or system according to any of the foregoing embodiments, wherein the bright-field illumination optics in the adapter are configured to receive and deflect a light beam emitted by the light source in order to back-illuminate the sample at a perpendicular angle of incidence.

[0093] C7. The adapter or system according to any of the foregoing embodiments, wherein the optical box further includes a lens mounted therein and aligned with the camera of the mobile device, the lens magnifying the image captured by the camera.

[0094] C8. The adapter or system according to any of the foregoing embodiments, wherein the image captured by the camera is further processed by the processor of the mobile device and the analysis results are output on the screen of the mobile device.

[0095] C9. The adapter or system according to any of the foregoing embodiments, wherein the lever is slidable and configured to realize both bright field illumination and fluorescent illumination optics in the same optical adapter.

[0096] C10. The adapter or system according to any of the foregoing embodiments, wherein the optical elements of the fluorescent illumination optics are mounted on a lever, and when the lever is fully slid into the optical housing,

[0097] C11. The adapter or system according to any of the foregoing embodiments, wherein a lever having a fluorescent illumination optics element blocks the light path of a bright field illumination optics and switches the illumination optics to a fluorescent illumination optics element.

[0098] C12. The adapter or system according to any of the foregoing embodiments, wherein when the lever slides out, the fluorescent illumination optics mounted on the lever move out of the optical path and switch the illumination optics to a bright field illumination optics.

[0099] C13. The adapter or system according to any of the foregoing embodiments, wherein the lever comprises two planes at different heights.

[0100] C14. The adapter or system according to any of the foregoing embodiments, wherein the two planes are connected together by a vertical rod and move together into or out of the optical box.

[0101] C15. The adapter or system according to any of the foregoing embodiments, wherein the two planes are separable and each plane can be individually moved into or out of the optical box.

[0102] C16. The adapter or system according to any of the foregoing embodiments, wherein the upper lever plane includes at least one optical element, which may be, but is not limited to, a filter.

[0103] C17. The adapter or system according to any of the foregoing embodiments, wherein the upper rod plane moves below the light source, and the preferred distance between the upper rod plane and the light source is in the range of 0 to 5 mm.

[0104] C18. The adapter or system according to any of the foregoing embodiments, wherein a portion of the bottom lever plane is not parallel to the image plane.

[0105] C19. The adapter or system according to any of the foregoing embodiments, wherein the surface of the non-parallel portion of the bottom lever plane has a mirror finish with a reflectivity greater than 95%.

[0106] C20. The adapter or system according to any of the foregoing embodiments, wherein a non-parallel portion of the bottom lever plane moves below the light source and deflects light emitted from the light source to provide reverse illumination of the sample area directly below the camera.

[0107] C21. An adapter or system according to any of the foregoing embodiments, wherein the preferred tilt angle of the non-parallel portion of the bottom lever plane is in the range of 45 degrees to 65 degrees, and the tilt angle is defined as the angle between the non-parallel bottom plane and the vertical plane.

[0108] C22. The adapter or system according to any of the foregoing embodiments, wherein a portion of the bottom lever plane is parallel to the image plane and is located below the sample and 1 mm to 10 mm away from the sample.

[0109] C23. The adapter or system according to any of the foregoing embodiments, wherein the surface of the parallel portion of the bottom lever plane is highly light-absorbing, having a light absorption of more than 95%.

[0110] C24. The adapter or system according to any of the foregoing embodiments, wherein the absorbing surface is used to eliminate reflected light that is back-illuminated on the sample at a small incident angle.

[0111] C25. The adapter or system according to any of the foregoing embodiments, wherein the lever includes a stop configured to stop the lever.

[0112] C26. The adapter or system according to any of the foregoing embodiments, wherein the stop includes a ball plug and uses a groove on the lever to stop the lever at a predetermined position when pulled outward from the adapter.

[0113] C27. The adapter or system according to any of the foregoing embodiments, wherein the stop is configured to allow the user to pull the lever with any force, but to stop the lever at a fixed position, at which the operating mode of the optical adapter switches to bright field illumination.

[0114] C28. The adapter or system according to any of the foregoing embodiments, wherein the sample slider is mounted in the receiver slot to receive the QMAX device and position the sample within the field of view and focus of the smartphone camera in the QMAX device.

[0115] C29. The adapter or system according to any of the foregoing embodiments, wherein the movable arm switches between two stop positions by pressing the QMAX device and the movable arm together to the end of the track groove and then releasing them.

[0116] C30. The adapter or system according to any of the foregoing embodiments, wherein the movable arm can indicate whether the QMAX device is inserted in the correct orientation.

[0117] C31. The adapter or system according to any of the foregoing embodiments, wherein the shape of one corner of the QMAX device is configured differently from the other three right-angle corners.

[0118] C31. The shape of the movable arm matches the corner shape of a specific shape, so that the QMAX device can only slide in the correct direction to the correct position in the track groove.

[0119] C32. The adapter or system according to any of the foregoing embodiments, wherein the sample slider comprises a fixed track frame and a movable arm:

[0120] C33. The adapter or system according to any of the foregoing embodiments, wherein a frame track is fixedly mounted in the receiver slot of the optical box; the track frame has a slide rail groove that matches the width and thickness of the QMAX device, allowing the QMAX device to slide along the track. The width and height of the track groove are carefully configured such that the QMAX device moves less than 0.5 mm in a direction perpendicular to the sliding plane and less than 0.2 mm along the thickness direction of the QMAX device.

[0121] C34. The adapter or system according to any of the foregoing embodiments, wherein the frame track has an open window below the field of view of the smartphone's camera to allow backlighting of the sample.

[0122] C35. The adapter or system according to any of the foregoing embodiments, wherein the movable arm is pre-built in the slide groove of the track frame and moves together with the QMAX device to guide the movement of the QMAX device in the track frame.

[0123] C36. The adapter or system according to any of the foregoing embodiments, wherein the movable arm is equipped with a stop mechanism having two predetermined stop positions.

[0124] B. Optical adapter (tilted fiber end illumination) for connecting a colorimeter reader to a smartphone.

[0125] Colorimetric determination is a powerful technique with wide applications in health monitoring, disease diagnosis, and chemical analysis. A key factor in obtaining accurate colorimetric results is the accurate quantification of color changes. Typically, the color change of a colorimetric test strip is analyzed by comparing it to a standard color chart. However, this comparison is performed by the human eye and is easily affected by ambient light conditions, which limits the accuracy of quantifying color changes.

[0126] The invention described herein addresses this problem by providing a system comprising an optical adapter and a mobile phone. The optical adapter is mounted on a mobile phone, which is then converted into a colorimetric reader. This reader provides consistent and uniform illumination to the front surface of the colorimetric test card and captures an image of the sample for color change analysis. The system can be conveniently and reliably operated by ordinary personnel in any location. The optical adapter utilizes existing resources of smartphones, including a camera, light source, processor, and display, providing a low-cost solution for accurately quantifying color changes in colorimetric measurements.

[0127] In this invention, the optical adapter includes a retainer frame that fits onto the upper part of the mobile phone and an optical box attached to the retainer. The optical box has a sample receiver slot and illumination optics. In some prior art mobile phone connection adapters, the adapter design is an integral piece including clamping mechanical parts and functional elements that fit onto the mobile phone. The problem with this design is that it requires redesigning the entire adapter for each specific smartphone model. However, in this invention, the optical adapter is divided into a retainer frame specifically for assembling the smartphone and a universal optical box containing all functional components. For smartphones of different sizes, as long as the relative positions of the camera and light source are the same, only the mounting bracket needs to be redesigned, saving significant design and manufacturing costs.

[0128] The optical adapter's optical housing includes: a receiver slot that receives the colorimetric sample and positions it within the field of view and focal range of a smartphone camera; and illumination and imaging optics that produce uniform illumination on the sample and capture an image of the sample independently of any external conditions.

[0129] To capture sample images accurately representing color changes, it is desirable for the sample area directly beneath the camera to be uniformly illuminated. However, for all ordinary smartphones, there is always a distance between the light source and the camera. When the sample is placed very close to the smartphone's camera, without additional illumination optics, the area uniformly frontally illuminated by the light source is directly below the light source but outside the camera's field of view. To address this issue, this invention uses a tilted, large-core optical fiber to rotate the beam emitted from the light source, ensuring uniform illumination of the sample area directly below the camera.

[0130] Furthermore, to produce more uniform illumination, a beam from a localized light source rather than a point LED source from a smartphone is desired. For this purpose, a separate diffuser could be provided in front of the fiber end face, but this approach increases the number of components in the optical adapter and raises costs. Instead, in this invention, both end faces of the fiber are given a matte finish to function as diffusers, allowing the end face facing the sample to become a surface light source for producing more uniform illumination on the sample.

[0131] Typically, the optical box also includes a lens mounted within it, aligned with the smartphone's camera to keep the sample within the camera's focal range. The image captured by the camera is further processed by the smartphone's processor to analyze color changes and output the analysis results on the smartphone's screen.

[0132] The sample slider is installed in the receiver slot to receive the QMAX device and position the sample within the QMAX device, which is within the field of view and focus range of the smartphone camera.

[0133] The sample slider consists of a fixed track frame and a movable arm:

[0134] The frame track is fixedly mounted in the receiver slot of the optical box. The track frame has slide grooves that match the width and thickness of the QMAX device, allowing the QMAX device to slide along the track. The width and height of the track grooves are carefully constructed such that the QMAX device moves less than 0.5 mm in the direction perpendicular to the sliding plane and less than 0.2 mm along the thickness direction of the QMAX device.

[0135] The frame track has an open window in the field of view of the phone's camera to allow light to reflect back onto the sample.

[0136] The movable arm is pre-set in the slide rail groove of the track frame and moves together with the QMAX device to guide the movement of the QMAX device in the track frame.

[0137] The movable arm is equipped with a stop mechanism having two predetermined stopping positions. In one position, the arm will stop the QMAX device at a location where the fixed sampling area on the QMAX device is exactly below the smartphone's camera. In the other position, the arm will stop the QMAX device at a location where the sampling area on the QMAX device is outside the smartphone's field of view, and the QMAX device can be easily removed from the track slot.

[0138] By pressing the QMAX device and the movable arm together to the end of the track groove and then releasing, the movable arm switches between two stop positions.

[0139] The movable arm indicates whether the QMAX device is inserted in the correct direction. One corner of the QMAX device is configured to be different from the other three right angles. The shape of the movable arm matches the corner shape of this specific configuration, ensuring that the QMAX device can only slide into the correct position in the track groove in the correct direction.

[0140] Figure 10A , 10B Figures 10 and 10C are schematic diagrams of system 10 for a smartphone colorimeter reader. Specifically, Figure 10B and 10C These are exploded views of system 10 shown from the front and rear sides, respectively. System 10 includes a smartphone 1; an optical adapter device 13 mounted on the upper part of the smartphone 1; and a colorimetric test card 137 inserted into a receiver slot 136 of the device 13 such that the sample area on the sample card 137 is within the field of view and focal range of the camera module 1C in the smartphone 1. Software (not shown) installed in the smartphone 1 analyzes the image collected by the camera module 1C while the light source 1L in the smartphone 1 is emitting light, in order to analyze the color changes of the colorimetric test, and outputs the results to the display screen 1f in the smartphone 1.

[0141] Figure 11 This is a schematic exploded view of the optical adapter device 13 in system 10. Device 13 includes a bracket housing 131 mounted on the upper part of smartphone 1; an optical box 132 attached to the housing 131 includes a receiver slot 136 and an optical chamber 132C. An optical insert 134 is fitted into the top of the optical chamber 132C, which has connections to the light source 1L and camera 1C in smartphone 1. Figure 10B (As shown in the diagram) Aligned exit aperture 134L and entrance aperture 134C. Lens 133 is mounted in entrance aperture 134C within optical insert 134 and is configured such that the sample area on colorimetric sample card 137 inserted into receiver slot 136 is within the working distance of camera 1C (e.g., ...). Figure 10B(As shown). The bulk-core fiber 135 is mounted at an angle in the exit aperture 134L. This gives the two end faces of the fiber 135 a matte finish. The operation of the fiber 135 as an illumination optics device in the apparatus 13 is described below in Figure 2.

[0142] Figure 12 This is a schematic cross-sectional view showing details of the system 10 for reading color charts, particularly device 13. The figure illustrates the above references. Figure 11 The functions of the described components are as follows: A light source 1L emits a light beam B1 away from the smartphone 1. The light beam B1 is connected to an optical fiber 135 through a first end face and travels along the direction of the optical fiber 135, and is emitted from a second end face to become a light beam B2. The light beam B2 illuminates the sample area of ​​the colorimetric sample card 137 directly below the camera 1C from the front to produce uniform illumination. Because the end face of the optical fiber 135 is made with a matte and diffuse finish, the light beam B2 can be considered to be emitted from a surface light source, which helps to produce more uniform illumination. The tilt angle of the optical fiber 135 is set so that the central ray of the light beam B2 illuminates the area on the sample card 137 directly below the camera. The lens 11 generates an image of the sample area on the image sensor plane of the camera 1C. The smartphone 1 captures and processes the image to analyze the color information in the image, thereby quantifying the color change of the colorimetric determination.

[0143] C. Optical adapter (fiber optic ring illumination) for connecting a colorimeter reader to a smartphone.

[0144] Colorimetric determination is a powerful technique with wide applications in health monitoring, disease diagnosis, and chemical analysis. A key factor in obtaining accurate colorimetric results is the accurate quantification of color changes. Typically, the color change of a colorimetric test strip is analyzed by comparing it to a standard color chart. However, this comparison is performed by the human eye and is easily affected by ambient light conditions, which limits the accuracy of quantifying color changes.

[0145] The invention described herein addresses this problem by providing a system comprising an optical adapter and a mobile phone. The optical adapter is mounted on a mobile phone, which is then converted into a colorimetric reader. This reader provides consistent and uniform illumination to the front surface of the colorimetric test card and captures an image of the sample for color change analysis. The system can be conveniently and reliably operated by ordinary personnel in any location. The optical adapter utilizes existing resources of smartphones, including a camera, light source, processor, and display, providing a low-cost solution for accurately quantifying color changes in colorimetric measurements.

[0146] In this invention, the optical adapter includes a retainer frame that fits onto the upper part of the mobile phone and an optical box attached to the retainer. The optical box has a sample receiver slot and illumination optics. In some prior art mobile phone connection adapters, the adapter design is an integral piece including clamping mechanical parts and functional elements that fit onto the mobile phone. The problem with this design is that it requires redesigning the entire adapter for each specific smartphone model. However, in this invention, the optical adapter is divided into a retainer frame specifically for assembling the smartphone and a universal optical box containing all functional components. For smartphones of different sizes, as long as the relative positions of the camera and light source are the same, only the mounting bracket needs to be redesigned, saving significant design and manufacturing costs.

[0147] The optical adapter's optical housing includes: a receiver slot that receives the colorimetric sample and positions it within the field of view and focal range of a smartphone camera; and illumination and imaging optics that produce uniform illumination on the sample and capture an image of the sample independently of any external conditions.

[0148] To capture sample images that accurately represent color changes, it is desirable for the sample area under the camera to be uniformly illuminated. However, for all typical smartphones, the light source is always a point source and mounted at a certain distance from the camera, meaning the light source is not centrosymmetric relative to the camera. This leads to the problem that when the sample is placed very close to the smartphone camera, without the aid of additional illumination optics, the illumination pattern on the front surface of the sample in the camera's field of view will have gradient intensity changes in a linear direction. Therefore, it is desirable to generate a light source with a large emission area and centrosymmetry with the camera. To achieve this, in this invention, a plastic side-emitting fiber optic ring is placed around the smartphone camera so that the fiber optic ring is centrosymmetric with respect to the camera. The two end faces of the fiber optic ring are mounted facing the smartphone's light source. This transforms the original single point source into an infinite number of small light sources with nearly equal luminous intensities distributed on a circle equidistant from the smartphone camera. Light emitted from the sidewalls of the ring fiber further passes through a diffuser film to increase the emission area and make the illumination more uniform. The sample area directly below the camera is uniformly frontally illuminated by an illumination optics based on the side-emitting fiber optic ring.

[0149] Because the representation of the colorimetric sample's color largely depends on the lighting conditions, it is important to control the illumination consistency within the optical box independently of any external light conditions. To address this, the receiver slot has a rubber door attached to it that completely covers the slot to prevent ambient light from entering the optical box and thus altering the lighting conditions.

[0150] Typically, the optical box also includes a lens mounted within it, aligned with the smartphone's camera to keep the sample within the camera's focal range. The image captured by the camera is further processed by the smartphone's processor to analyze color changes and output the analysis results on the smartphone's screen.

[0151] The sample slider is installed in the receiver slot to receive the QMAX device and position the sample within the QMAX device, which is within the field of view and focus range of the smartphone camera.

[0152] The sample slider consists of a fixed track frame and a movable arm:

[0153] The frame track is fixedly mounted in the receiver slot of the optical box. The track frame has slide grooves that match the width and thickness of the QMAX device, allowing the QMAX device to slide along the track. The width and height of the track grooves are carefully constructed such that the QMAX device moves less than 0.5 mm in the direction perpendicular to the sliding plane and less than 0.2 mm along the thickness direction of the QMAX device.

[0154] The frame track has an open window in the field of view of the phone's camera to allow light to reflect back onto the sample.

[0155] The movable arm is pre-set in the slide rail groove of the track frame and moves together with the QMAX device to guide the movement of the QMAX device in the track frame.

[0156] The movable arm is equipped with a stop mechanism having two predetermined stopping positions. In one position, the arm will stop the QMAX device at a location where the fixed sampling area on the QMAX device is exactly below the smartphone's camera. In the other position, the arm will stop the QMAX device at a location where the sampling area on the QMAX device is outside the smartphone's field of view, and the QMAX device can be easily removed from the track slot.

[0157] By pressing the QMAX device and the movable arm together to the end of the track groove and then releasing, the movable arm switches between two stop positions.

[0158] The movable arm indicates whether the QMAX device is inserted in the correct direction. One corner of the QMAX device is configured to be different in shape from the other three right angles. The shape of the movable arm matches the specific corner shape, ensuring that the QMAX device can only slide into the correct position in the track groove in the correct direction.

[0159] Some implementation plans

[0160] 1. Fiber optic ring illuminator

[0161] In some implementations of optical components, where

[0162] a. The radius of the side-emitting optical fiber is 10 mm;

[0163] b. The diameter of the ring fiber can be at least 5mm, 10mm, 15mm, 20mm, 25mm, 30mm, 40mm, 50mm, 60mm, 80mm or 100mm, or within any two values;

[0164] c. The diameter of the cross-section of the ring fiber can be at least 0.5 mm, 1.0 mm, 1.5 mm, 2.0 mm, 2.5 mm, 3 mm, 4 mm, 5 mm, 6 mm, 8 mm or 10 mm, or within any two values.

[0165] In some implementations of optical components, where

[0166] d. The diameter of the external imager lens is 6mm;

[0167] e. The diameter of the imager lens may be at least 2 mm, 3 mm, 4 mm, 5 mm, 10 mm, 15 mm, 20 mm, 25 mm, 30 mm, 40 mm or 50 mm, or within any two values.

[0168] In some implementations of the optical component, the ring fiber can be used in conjunction with a microlens array or replaced by a microlens array;

[0169] In some embodiments of the optical component, the optical component includes a light diffuser plate between the sample and the annular optical fiber, wherein the light diffuser plate has an aperture configured to be aligned with a camera.

[0170] In some embodiments of the optical component, the length of one side of the light diffuser can be at least 5 mm, 10 mm, 15 mm, 20 mm, 25 mm, 30 mm, 40 mm, 50 mm, 100 mm, 150 mm or 200 mm, or within any two values, and the thickness of the diffuser can be at least 2 mm, 3 mm, 4 mm, 5 mm, 10 mm, 15 mm or 20 mm, or within any two values.

[0171] In some implementations of the optical component, the distance between the light diffuser and the ring-shaped optical fiber can be at least 1 mm, 10 mm, 15 mm, 20 mm, 25 mm, 30 mm, 40 mm, 50 mm, 100 mm, or within any two values.

[0172] The optical component of claim 2, wherein the distance between the sample and the annular fiber can be at least 2 mm, 10 mm, 15 mm, 20 mm, 25 mm, 30 mm, 40 mm, 50 mm, 100 mm, 150 mm, or 200 mm, or within any two values.

[0173] lever:

[0174] 1. The optical component of claim 3, wherein the distance between the first plane on the movable arm and the light source can be at least 0.5 mm, 2 mm, 4 mm, 8 mm, 10 mm, 20 mm, 50 mm, 100 mm or within any two values.

[0175] 2. The optical component of claim 3, wherein the distance between the first plane and the second plane of the movable arm can be at least 5 mm, 10 mm, 15 mm, 20 mm, 40 mm, 100 mm, or 200 mm, or within any two values.

[0176] 3. The optical component of claim 5, wherein the distance by which the movable arm needs to move to switch between different positions can be at least 1 mm, 5 mm, 15 mm, 20 mm, 40 mm, 100 mm, or within any two values.

[0177] 4. The optical component of claim 3, wherein the second plane is connected to the tilted plane, and the mirror is mounted on the tilted plane. 5. The optical component of claim 4, wherein the preferred tilt angle of the tilted plane may be at least 10 degrees, 30 degrees, 60 degrees, 80 degrees, or within any two values, and the tilt angle is defined as the angle between the second plane and the tilted plane.

[0178] Figure 13A , 13B Figures 1 and 13C are schematic diagrams of system 10 for a colorimeter reader in a smartphone. Specifically, Figure 13B and Figure 13CThese are exploded views of system 10, shown from the front and rear sides, respectively. System 10 includes a smartphone 1; an optical adapter device 13 mounted on the upper part of the smartphone 1; and a colorimetric sample card 138, which is inserted into the receiver slot 137 of the device 13 such that the sample area on the sample card 138 is within the field of view and focus of the camera module 1C in the smartphone 1. After the sample card 138 is inserted, a rubber door 139 attached to the device 18 covers the receiver slot 137 to prevent ambient light from entering the optical adapter 13 and affecting the test. Software (not shown) installed in the smartphone 1 analyzes the image collected by the camera module 1C while the light source 1L in the smartphone 1 is emitting light, in order to analyze the color changes of the colorimetric test, and outputs the results to the display screen 1f in the smartphone 1.

[0179] Figure 14 This is a schematic exploded view of the optical adapter device 13 in system 10. Device 13 includes a bracket housing 131 mounted on the upper part of the smartphone 1; an optical box 132 attached to the housing 131 includes a receiver slot 137, an optical chamber 132C, and a rubber door 139, which is inserted into the groove 137 to cover the receiver slot 137. An optical insert 134 is fitted into the top of the optical chamber 132C, which has connections to the light source 1L and camera 1C in the smartphone 1. Figure 13B (As shown in the diagram) Aligned exit aperture 134L and entrance aperture 134C. Lens 133 is mounted in entrance aperture 134C within optical insert 134 and is configured such that the sample area on colorimetric sample card 138 inserted into receiver slot 137 is within the working distance of camera 1C (e.g., ...). Figure 13B (As shown). A side-emitting fiber optic ring 135 is mounted in an optical insert 134, which is configured to center the camera 1C within the fiber optic ring 135. The two end faces of the fiber optic ring 135 are mounted in an exit aperture 134L facing the light source 1L. A light-diffusing film 136 is placed below the fiber optic ring 135 and has an aperture for opening the lens aperture. The fiber optic ring 135, which operates as the illumination light in the device 13, is shown below. Figures 15A to 15C As described in the text.

[0180] Figure 15A , 15B Figures 15C and 15C show schematic diagrams detailing the system 10 for reading color charts, particularly the device 13. Figure 15A This is a cross-sectional view showing details of device 13. And... Figure 15B and Figure 15C These are schematic diagrams showing only the construction of the optical elements in device 13. These figures illustrate the above references. Figure 14The functions of the described components are as follows: Light emitted from the light source 1L is coupled from both end faces of the fiber optic ring 135 to the side-emitting fiber optic ring 135 and propagates along the inside of the ring. Beam B1 exits from the sidewall of the fiber optic ring and passes through the diffuser film 136. Beam B1 illuminates the sample area of ​​the colorimetric sample card 138 directly below the camera 1C from the front to produce uniform illumination. The illuminated sample area absorbs part of beam B1 and reflects beam B1 into beam B2. Beam B2 is collected by lens 133 and enters the camera 1C. Lens 133 generates an image of the sample area on the image sensor plane of the camera 1C. The smartphone 1 captures and processes the image to analyze the color information in the image, thereby quantifying the color change in the colorimetric determination.

[0181] D. Tomographic imaging devices and systems

[0182] D-1. QMAX Structural Tomography Device

[0183] A tomographic device for reconstructing sliceable virtual 3D copies of biological samples at the highest resolution at the nanoscale is disclosed. The device includes an imaging sensor, lenses, and a QMAX device, such as... Figure 16A As shown.

[0184] The QMAX device features a periodic column array. The biological sample is contained within the QMAX device. A refractive index-matching liquid is used to reduce light scattering and minimize inhomogeneities in the refractive index across the sample. The QMAX structure enhances detection sensitivity by six (or more) orders of magnitude.

[0185] D-2. Calibration based on QMAX structure

[0186] The column array has a metal disk at the top of each column. The metal disk provides calibration signals for spatial and height calibration of the image captured by the imaging sensor. The shape of the metal disk can be designed to facilitate rapid calibration. For example, the shape of the metal disk could resemble the letter E; this column array... Figure 16B As shown in the image.

[0187] When the imaging sensor captures images of a QMAX structure with or without biological samples, the captured images can be spatially calibrated, and the camera's focal length can also be quantitatively calibrated.

[0188] For spatial calibration, the captured image undergoes object detection. Object detection schemes can include template matching, optical character recognition, shape detection, or other schemes used in this field. Object detection retrieves the orientation of the detected pattern. Figure 16B In this embodiment, the direction is represented by the letter E. Spatial calibration is achieved through two-dimensional geometric transformation using orientation parameters.

[0189] We disclose a quantitative calibration of the focal length using a column array. The effect of focal length on the captured image can be explained using a thin lens model, such as... Figure 16C As shown. If the sensing device is a certain distance from the focal plane, point Q will be projected onto a circle of diameter kσ, and its emissivity will spread along the circle, where Q is defocused. The position v of the focal plane depends on the focal length f of the lens and the distance u from the object. The relationship between these three variables is given by the well-known Gaussian lens law or thin lens equation:

[0190] We measure the degree of focus on the captured image and deduce the location of the focus plane. Focus degree measures the level of focus of the entire image or each pixel in the image. Various algorithms and operators have been proposed in the literature to measure focus degree, such as gradient-based, Laplacian operator-based, wavelet-based, statistical, cosine transform / Fourier transform-based, and so on.

[0191] The focus of the column array captured at different focal planes can be pre-measured and stored in a lookup table. For example, when the imaging sensor captures a new image of the column array, Figure 16D It shows Figure 16B Using the example column array captured image, we calculate the focus of the newly captured image, refer to the focus lookup table, and find its corresponding focal plane position.

[0192] D-3. Tomography System

[0193] The purpose of tomography is to reconstruct the three-dimensional volume of a biological sample through multiple projections. An end-to-end tomography system includes a light source, imaging, and 3D reconstruction.

[0194] light source

[0195] Light captured by an imaging sensor can be refracted from the sample, emitted from the sample, etc.

[0196] Imaging

[0197] The imaging section captures the projection onto the imaging sensor. Projections can be captured at different focal lengths, angles, and from different lighting conditions.

[0198] Several images can be captured at different focal lengths. The lens moves toward or backward in steps or multiple steps within the QMAX structure. The step size and lens movement can be controlled by hardware or software via an application programming interface. The image sensor records the captured images.

[0199] Several images can be captured at different angles. The sample is rotated and an optical image is captured through its approximately linear projection. The sample is rotated to a series of angular positions, and an image is captured in each orientation. The device is carefully aligned to ensure the rotation axis is perpendicular to the optical axis, allowing the imaging sensor to collect projection data about each plane. The focal plane can be located midway between the rotation axis and the QMAX card closest to the lens. This means that each image contains both focused data from the front half of the sample (the half closest to the lens) and defocused data from the rear half. The focused data is used for 3D volumetric reconstruction, while the defocused data is not used. A bandpass filter can be equipped to select the focused data.

[0200] Optical projection tomography is performed using a standard tomographic algorithm. Due to the position of the focal plane relative to the rotation axis, two images taken 180 degrees apart will focus on different parts of the sample. Limiting the back projection to the region corresponding to the focused portion of the sample improves the quality of the results. When accumulating data through various orientations of the sample, the half-disc mask used as a bandpass filter can be rotated to ensure that only the focused data is back-projected.

[0201] Several images can be captured under different illuminations. A quantitative phase image can be obtained from the time-correlated interferometry pattern caused by the frequency shift of the reference beam relative to the sample beam. A tilting mirror equipped with a galvanometer can be used to change the illumination angle. The laser beam passes through two acousto-optic modulators that shift the laser beam frequency. A second beam splitter recombines the sample and reference laser beams, forming an interference pattern captured at the imaging sensor. The phase image is then calculated by applying phase-shifting interferometry. For near-plane wave illumination of thin samples with low refractive index contrast, the phase of the transmitted field is well approximated by the line integral of the refractive index along the beam propagation path. Therefore, the phase image can be simply interpreted as a projection of the refractive index.

[0202] In addition to bandpass filters, various imaging filters can be used during image capture for (including but not limited to) the following purposes:

[0203] (1) Signal selection, thereby selecting a portion of the captured image;

[0204] (2) Signal enhancement, thereby enhancing part or all of the captured image;

[0205] (3) Signal transformation, thereby transforming part or all of the captured image into another representation, such as frequency representation, multi-scale representation, etc.

[0206] (4) Signal copying, thereby replacing a portion of the captured image with another portion of the captured image, or with a representation of another portion of the captured image;

[0207] (5) or any combination of (1)-(4).

[0208] By performing filtering processes such as contrast enhancement, color enhancement, and noise reduction on the acquired images, the dynamic range of pixel brightness can be improved, color temperature can be adjusted, and the signal-to-noise ratio can be increased.

[0209] The captured image can be converted into another representation that is more suitable for 3D reconstruction. It can be converted into different formats (8-bit to 16-bit, integer to floating-point, etc.), different color spaces (RGB to HSV, etc.), different domains (spatial domain to frequency domain, etc.), etc.

[0210] A portion of a captured image can be replaced by another portion (or a transformation of that other portion). This could be a spatial region replaced by a transformation of another region, such as reflection extensions around a boundary, etc.; it could be a frequency sub-band replaced by a transformation of another frequency sub-band, such as a high-frequency sub-band being replaced by an estimate from a low-frequency sub-band, etc.

[0211] 3D Reconstruction

[0212] Reconstructing the three-dimensional volume of a biological sample from its projection is an inverse problem. Three-dimensional volume reconstruction can employ phase image retrieval schemes, backprojection schemes, nonlinear approximation schemes, optimization schemes, and more.

[0213] When capturing several images at different focal distances, we calculate the focus of these images and list these focus values ​​as vectors. We then use a lookup table to reference these vectors and find their corresponding focal plane distances. These distances can be based on distance, correlation, or other criteria, such as selecting the best match.

[0214] Figure 16E A diagram of a phase image retrieval-based scheme is shown. It consists of four components:

[0215] Focal length calculation

[0216] • Phase image retrieval

[0217] • Height estimate

[0218] · 3D volume reconstruction

[0219] The second component, phase retrieval, is a quantitative phase imaging technique based on the Intensity Transmission (TIE) equation. (TIE equation state)

[0220]

[0221] in This represents the intensity gradient that can be calculated from a multifocal image, where k is the wavenumber. It is the sample phase distribution.

[0222] The TIE equations can be solved using Fast Fourier Transform (FFT) and Discrete Cosine Transform (DCT); for example, "Boundaryless Artifact Phase Retrieval Using the Transmission of the Intensity Equation: Fast Solution Using Discrete Cosine Transform," C. Zuo, Q. Chen, and A. Asundi, Optics Express, Vol. 22, No. 8, April 2014. Retrieving Phase Images from TIE Equations.

[0223] Given a phase image, we estimate the height (thickness) of a biological sample. Recall that for a sample with thickness t and refractive index n, the corresponding optical path length Lp is...

[0224] L p =t×n

[0225] The height of a biological sample can be calculated using a known refractive index.

[0226] Furthermore, the three-dimensional volume of biological samples can be reconstructed.

[0227] Back projection algorithms are commonly used for 3D reconstruction in tomography. They include Fourier transform basis algorithms, filtered back projection algorithms, back projection filtering algorithms, and iterative algorithms.

[0228] When the focal plane is positioned differently relative to the rotation axis, two images taken 180 degrees apart will focus on different parts of the sample. To compensate for this, a back projection algorithm with half-plane adjustment can be used. Therefore, limiting the back projection to the region corresponding to the focused portion of the sample will improve the quality of the results. When accumulating data through various orientations of the sample, the half-disc mask can be rotated to ensure that only the focused data is back-projected.

[0229] As another implementation of the back-projection algorithm, a process based on a filtered back-projection method can be applied. A discrete inverse Radon transform is applied to each x-slice along the beam rotation direction, where x is the coordinate in the tilt direction and the relative angle between the laser beam direction and the objective optical axis. To compensate for the angle between the imaging and illumination directions, the x-value is divided by . To reduce the influence of missing projections, an iterative constraint method can be applied.

[0230] For the inversion problem of reconstructing a 3D volume from its projection, the resulting 3D volume may be blurry. Ramp filters can be used to eliminate or reduce the blur.

[0231] In addition to deblurring filters, various imaging filters can be used for 3D volume reconstruction, such as (but not limited to):

[0232] (1) Signal selection, where an image or a portion of an image volume is selected;

[0233] (2) Signal enhancement, wherein a portion or all of an image or image volume is enhanced;

[0234] (3) Signal transformation, thereby transforming part or all of the captured image into another representation, such as frequency representation, multi-scale representation, etc.

[0235] (4) Signal copying, thereby replacing a portion of the captured image with another portion of the captured image, or with a representation of another portion of the captured image;

[0236] (5) or any combination of (1)-(4).

[0237] D-4. Embodiments of the Invention

[0238] DA1. An apparatus for sample imaging, comprising a QMAX device and an imager, wherein:

[0239] (1) The QMAX device includes:

[0240] The first plate, the second plate, and the spacer, wherein:

[0241] i. The plates can be moved relative to each other to form different configurations;

[0242] ii. One or both plates are flexible;

[0243] iii. Each plate includes a sample contact area on its inner surface for contacting the fluid sample;

[0244] iv. One or two plates include spacers fixed to the respective plates;

[0245] v. The spacers have a predetermined substantially uniform height and a predetermined spacer spacing, and

[0246] vi. At least one spacer is located inside the sample contact area;

[0247] One of these structures is an open structure, in which: the two plates are separate, the spacing between the plates is not adjustable by the spacers, and the sample is deposited on one or both plates; and

[0248] Another aspect of the construction is a closed structure constructed in an open structure after sample deposition; and in the closed structure: at least a portion of the sample is compressed into a layer of uniform thickness by two plates, wherein the uniform thickness of the layer is limited by the inner surfaces of the two plates and adjusted by the plates and spacers.

[0249] (2) The imager is configured to capture an image of a signal emitted from at least a portion of a layer of uniform thickness.

[0250] DB1. A system for computed tomography, comprising a QMAX device, an imager, a holder, and a control device, wherein:

[0251] (1) The QMAX device includes: a first plate, a second plate, and a spacer, wherein:

[0252] i. The plates can be moved relative to each other to form different configurations;

[0253] ii. One or both plates are flexible;

[0254] iii. Each plate includes a sample contact area on its inner surface for contacting the fluid sample;

[0255] iv. One or two plates include spacers fixed to the respective plates;

[0256] v. The spacers have a predetermined substantially uniform height and a predetermined spacer spacing, and

[0257] vi. At least one spacer is located inside the sample contact area;

[0258] One of these structures is an open structure, wherein: the two plates are separate, the spacing between the plates is not adjustable by the spacers, and the sample is deposited on one or both of these plates; and

[0259] Another aspect of the construction is a closed structure constructed in an open structure after sample deposition; and in the closed structure: at least a portion of the sample is compressed into a layer of uniform thickness by two plates, wherein the uniform thickness of the layer is limited by the inner surfaces of the two plates and adjusted by the plates and spacers.

[0260] (2) The imager includes an image sensor and a lens, wherein:

[0261] i. The lens is configured to focus a signal emitted from at least a portion of a layer of uniform thickness and project the focused signal onto an image sensor, and

[0262] ii. An image sensor is configured to capture an image of the focus signal;

[0263] (3) The retainer is configured to adjust the relative position between the QMAX device and the imager; and

[0264] (4) The control device includes hardware and software for controlling and / or deriving positional adjustments made by the support, and for receiving the image and reconstructing it into a three-dimensional volume.

[0265] DBB1. A system for tomographic imaging, comprising a QMAX device, an imager, a holder, and a control device, wherein:

[0266] (1) The QMAX device includes: a first plate, a second plate, and a spacer, wherein:

[0267] i. The plates can be moved relative to each other to form different configurations;

[0268] ii. One or both plates are flexible;

[0269] iii. Each plate includes a sample contact area on its inner surface for contacting the fluid sample;

[0270] iv. One or two plates include spacers fixed to the respective plates;

[0271] v. The spacers have a predetermined substantially uniform height and a predetermined spacer spacing, and

[0272] vi. At least one spacer is located inside the sample contact area;

[0273] One of these configurations is an open configuration, wherein: the two plates are separate, the spacing between the plates is not adjustable by the spacer, and the sample is deposited on one or both plates; and

[0274] Another configuration is a closed configuration, which is formed after the sample is deposited in the open configuration; and in the closed configuration: at least a portion of the sample is compressed into a layer of uniform thickness by two plates, wherein the uniform thickness of the layer is defined by the inner surfaces of the two plates and adjusted by the plates and the spacer.

[0275] (2) The imager is capable of changing the focal plane and includes an image sensor and a lens, wherein:

[0276] i. The lens is configured to focus a signal emitted from at least a portion of the layer of uniform thickness and project the focused signal onto the image sensor, and

[0277] ii. The image sensor is configured to capture an image of the focus signal;

[0278] iii. The lens is a single lens or a composite lens composed of several lenses;

[0279] iv. At least one element in the lens is movable to change the distance from the image sensor, thereby changing the focal plane of the imager; and

[0280] v. The movable lens may be driven by a stepper motor and / or electromagnetic force, which may be computerized or manually controlled.

[0281] as well as

[0282] (4) The control device includes hardware and software for controlling and / or deriving positional adjustments made by the support, and for receiving the image and reconstructing it into a three-dimensional volume.

[0283] DC1. A tomographic imaging method, comprising the following steps:

[0284] (a) Deposit the sample onto the QMAX device in any of the foregoing device or system embodiments;

[0285] (b) Following (a), the two plates are used to compress at least a portion of the sample into a layer of substantially uniform thickness, the layer being constrained by the sample contact surfaces of the plates, wherein the uniform thickness of the layer is adjusted by the spacers and the plates, wherein the compression comprises:

[0286] Place the two boards together; and

[0287] A region of at least one of these plates is conformally pressed in parallel or sequentially to press the plates together into a closed configuration, wherein the conformal pressing on the plates produces substantially uniform pressure on at least a portion of the sample, and the pressing causes at least a portion of the sample to spread laterally between the sample contact surfaces of the plates, and wherein the closed configuration is a configuration in which the spacing between the plates in a uniform thickness region layer is adjusted by the spacers.

[0288] (c) Using an imager from any of the foregoing device or system embodiments, capture an image of the signal emitted from at least a portion of the layer of said uniform thickness;

[0289] (d) Adjust the relative position of the QMAX device and the imager, and repeat step (c); and

[0290] (e) Following a series of steps (c), the captured image is reconstructed into a three-dimensional volume of at least a portion of the layer of said uniform thickness.

[0291] Conformal pressing is a method that keeps the pressure applied to a region substantially constant and independent of changes in the shape of the outer surface of the plate; and

[0292] The parallel press simultaneously applies pressure to the intended area, while the sequential press applies pressure to a portion of the predetermined area and gradually moves to other areas.

[0293] DCC1. A method for capturing images at different focal planes, comprising the following steps:

[0294] (a) The movable lens in the imager is brought to its initial position by computer or manual control.

[0295] (b) Position the movable lens relative to the position of the focal plane;

[0296] (c) Use the image sensor in the imager to capture images and record the position of the focal plane;

[0297] (d) Computerize or manually add step displacements to move the movable lens to the next position;

[0298] (e) Repeat steps (b) to (d);

[0299] (f) After a series of steps (e), capture several images at different focal planes.

[0300] DA21. The apparatus according to any of the foregoing embodiments, wherein the QMAX apparatus further comprises a drying reagent coated on one or two plates, the drying reagent staining the sample.

[0301] DA22. The apparatus according to any of the foregoing embodiments, wherein:

[0302] i. One or two plate sample contact areas include one or more binding sites, each binding site binding and immobilizing its respective analyte; or

[0303] ii. One or two plate sample contact areas contain one or more storage sites, each storage site storing one or more reagents; wherein the reagents are dissolved and dispersed in the sample during or after step (c), and wherein the sample contains one or more analytes; or

[0304] iii. One or more amplification sites, each of which is capable of amplifying a signal from the analyte or its label when the analyte or label is 500 nm away from the amplification site.

[0305] iv. any combination of i to iii.

[0306] DA23. The apparatus according to any of the foregoing embodiments, wherein the imager further includes a light source that provides illumination or excitation light for imaging a uniform thickness layer.

[0307] DA24. The apparatus according to embodiment DA23, wherein the light source is selected from the group consisting of LEDs, lasers, incandescent lamps, and any combination thereof.

[0308] DB2. The system according to embodiment DB1, wherein the signal includes an optical signal selected from the group consisting of: light reflection, light refraction, light transmission, light emission signals, and any combination thereof.

[0309] DB3. The system according to any of the foregoing embodiments, wherein the imager further includes a light source that provides light to illuminate a uniform thickness layer for imaging, wherein the light source is selected from the group consisting of incandescent light, LED, CFL, laser, and any combination thereof.

[0310] DB4. The system according to any of the foregoing embodiments, wherein the imager further includes a light source that provides excitation light that excites fluorescence emission from the layer of uniform thickness used for imaging, wherein the light source is an LED and / or a laser.

[0311] DB5. The system according to any of the foregoing embodiments, wherein the retainer is capable of adjusting the relative position of the lens and the QMAX device along the optical axis of the QMAX device to change the focal plane position of the lens.

[0312] DB6. The system according to any of the foregoing embodiments, wherein the retainer is capable of adjusting the relative position between the lens and the QMAX device to change the imaging angle, wherein the imaging angle is the angle between the focal plane of the lens and the uniform thickness layer.

[0313] DB7. The system according to any of the foregoing embodiments, wherein the imager further includes a light source providing illumination light for imaging, and wherein the holder is capable of adjusting the relative position between the light source and the QMAX device to change the incident angle of the illumination light, wherein the incident angle is the angle between the illumination light and a line perpendicular to the uniform thickness layer.

[0314] DB8. The system according to any of the foregoing embodiments, wherein the control device includes hardware and software for sending a command defining a position adjustment to the retainer, and wherein the retainer is configured to receive the command and adjust with a deviation not exceeding 10%.

[0315] DB9. The system according to any of the foregoing embodiments, wherein the control device includes hardware and software for sending a command defining a position adjustment to the retainer, and wherein the retainer is configured to receive the command and adjust with a deviation not exceeding 1%.

[0316] DB10. The system according to any one of embodiments DB8-DB9, wherein the control device includes hardware and software for receiving input defining position adjustment and converting the input into commands for adjusting the retainer.

[0317] DB11. The system according to any of the foregoing embodiments, wherein the system further comprises a plurality of calibration columns, and wherein:

[0318] (1) Multiple calibration columns are located between the sample contact areas of the two plates of the closed structure, and have different heights from each other, all of which are less than the uniform height of the spacer.

[0319] (2) Capture the images at different focal planes along the common optical axis; and

[0320] (3) The control device includes hardware and software for: (a) calculating a focus score for each of the images; and (b) inferring the focus plane position of each of the captured images by comparing the focus score with a lookup table, wherein the focus score is a focus matrix calculated for each pixel of the captured image, wherein the lookup table is predetermined and includes a row of predetermined focus plane positions along a common optical axis and corresponding row of calibration focus scores, each calibration focus score being calculated based on an image of a calibration column captured at the corresponding predetermined focus plane.

[0321] DB12. The system according to any of the foregoing embodiments, wherein the images are captured at different focal planes along a common optical axis, and wherein the control device comprises hardware and software for: (a) generating a phase image for a biological entity in at least a portion of the layer, wherein the phase image is a phase distribution calculated based on the wavelength of illumination light used for imaging, at least a portion of an image containing signals from the biological entity, and the focal plane positions of the captured images; and (b) estimating the thickness of the biological entity based on the phase image and the refractive index of the sample, wherein the biological entity is part or all of at least a portion of the layer.

[0322] DB13. A system according to embodiment DB8, wherein the control device includes hardware and software for reconstructing said at least a portion of an image into a three-dimensional volume of a biological entity based on the estimated thickness.

[0323] DB14. The system according to any of the foregoing embodiments, wherein the images are captured at different imaging angles, wherein the control device includes hardware and software for: (1) knowing or deriving the imaging angle of each of the images; and (2) reconstructing the images into a three-dimensional volume based on the known / derived imaging angles using a rear projection algorithm, and wherein the imaging angle is the angle between the focal plane of the lens and the layer of the uniform thickness.

[0324] DB15. The system according to any of the foregoing embodiments, wherein images are captured at different incident angles of illumination light, wherein the control device includes hardware and software for: (1) knowing or deriving the incident angle of each image; and (2) reconstructing the image into a three-dimensional volume based on the known / derived incident angle using a back projection algorithm, and wherein the incident angle of illumination light is the angle between the illumination light and a line perpendicular to a uniform thickness layer.

[0325] DB16. The system according to any one of the implementation schemes DB14-DB15, wherein the back projection algorithm is selected from the group consisting of: Fourier transform basis algorithms, filtered back projection algorithms, back projection and filtering algorithms, iterative algorithms, and any combination thereof.

[0326] DB17. The system according to any of the foregoing embodiments, wherein the imager is equipped with an imaging filter, and wherein the captured image is software filtered by the imaging filter and / or control device for: (1) signal selection, thereby selecting a portion of the captured image; (2) signal enhancement, thereby enhancing part or all of the captured image; (3) signal transformation, transforming part or all of the captured image into another representation, such as a frequency representation, a multi-scale representation, etc.; (4) signal replication, thereby replacing a portion of the captured image with another portion of the captured image, or with a representation of another portion of the captured image; or any combination of (1)-(4).

[0327] DB18. The system according to any of the foregoing embodiments, wherein the control device further comprises hardware and software for reconstructing at least a portion of an image into a three-dimensional volume, wherein during the three-dimensional volume reconstruction, the image and the three-dimensional volume are filtered by software for: (1) signal selection, wherein a portion of the image or image volume is selected; (2) signal enhancement, wherein a portion or all of the image or image volume is enhanced; (3) signal transformation, wherein a portion or all of the image or image volume is transformed into another representation, such as a frequency representation, a multi-scale representation, etc.; (4) signal replication, wherein a portion of the image or image volume is replaced by another portion of the captured image, or by a representation of another portion of the captured image; or any combination of (1)-(4).

[0328] DC2. The method according to embodiment DC1 further includes: staining the sample with a staining agent before step (c).

[0329] DC3. The method according to any of the preceding method embodiments, wherein during step (b), the conformal pressure is performed by hand.

[0330] DC4. The method according to any of the preceding method embodiments, wherein the conformal pressing in step (d) is provided by a pressurized liquid, pressurized gas or conformal material.

[0331] DC5. The method according to any of the foregoing method embodiments, wherein the adjustment step (d) includes adjusting the relative position of the lens to the QMAX device along the optical axis of the QMAX device to change the focal plane position of the lens.

[0332] DC6. The method according to any of the foregoing method embodiments, wherein the adjustment step (d) includes adjusting the relative position between the lens and the QMAX device to change the imaging angle, wherein the imaging angle is the angle between the focal plane and the uniform thickness layer.

[0333] DC7. The method according to any of the foregoing method embodiments, wherein the imager further includes a light source for providing illumination light for imaging, and wherein the adjustment step (d) includes adjusting the relative position of the light source and the QMAX device to change the incident angle of the illumination light, wherein the incident angle is the angle between the illumination light and a line perpendicular to the uniform thickness layer.

[0334] DC8. The method according to any of the foregoing implementation schemes, wherein the adjustment step (d) is performed manually.

[0335] DC9. The method according to any of the preceding method embodiments, wherein the adjustment step (d) is performed by a control device operatively coupled to the retainer, wherein the control device includes hardware and software for receiving input defining the position adjustment and sending commands to the retainer, and wherein the retainer is configured to receive the commands and make the adjustment have a deviation of no more than 10%.

[0336] DC10. The method according to any of the preceding method embodiments, wherein the adjustment step (d) is performed by a control device operatively coupled to the retainer, wherein the control device includes hardware and software for receiving inputs defining the position adjustment and sending commands to the retainer, and wherein the retainer is configured to receive commands and make the adjustment have a deviation of no more than 1%.

[0337] DC11. The method according to any prior method implementation, wherein the images are captured at different focal planes along a common optical axis, and wherein the reconstruction step (e) comprises: (i) calculating a focus score for each of the images; and (ii) inferring the focal plane position of each of the captured images by comparing the focus scores with a lookup table, wherein the focus score is a focus matrix calculated for each pixel of the captured image, wherein the lookup table is predetermined and includes a row of predetermined focal plane positions along the common optical axis and corresponding rows of calibrated focus scores, each calibrated focus score being calculated based on an image of a calibration column captured at the corresponding predetermined focal plane.

[0338] DC12. The method according to any prior method embodiment, wherein the image is captured at different focal planes along a common optical axis, and wherein the reconstruction step (e) comprises: (i) generating a phase image for a biological entity in at least a portion of the layer, wherein the phase image is a phase distribution calculated based on the wavelength of illumination light used for imaging, at least a portion of the image containing a signal from the biological entity, and the focal plane position of the captured image; and (ii) estimating the thickness of the biological entity based on the phase image and the refractive index of the sample, wherein the biological entity is part or all of at least a portion of the layer.

[0339] DC13. The method according to embodiment DC12, wherein the reconstruction step (e) further comprises reconstructing at least a portion of the image into a three-dimensional volume of the biological entity based on the estimated thickness.

[0340] DC14. The method according to any of the foregoing method embodiments, wherein the images are captured at different imaging angles, wherein the reconstruction step (e) comprises: (i) knowing or deriving the imaging angle of each of the images; and (ii) reconstructing the images into a three-dimensional volume based on the known / derived imaging angles using a rear projection algorithm, and wherein the imaging angle is the angle between the focal plane of the lens and a layer of uniform thickness.

[0341] DC15. The method according to any of the foregoing method embodiments, wherein the images are captured at different incident angles of illumination light, wherein the reconstruction step (e) comprises: (i) knowing or deriving the incident angle of each of the images; and (ii) reconstructing the images into a three-dimensional volume based on the known / derived incident angles using a back projection algorithm, and wherein the incident angle of illumination light is the angle between the illumination light and a line perpendicular to a uniform thickness layer.

[0342] DC16. The method according to any one of the implementation schemes DC14-DC15, wherein the back projection algorithm is selected from the group consisting of: Fourier transform basis algorithms, filtered back projection algorithms, back projection and filtering algorithms, iterative algorithms, and any combination thereof.

[0343] DC17. The method according to any of the preceding method embodiments, wherein the sample is a biological sample selected from cells, tissues, body fluids, feces, and any combination thereof.

[0344] DC18. The method according to any of the preceding method implementation schemes, wherein the sample is an environmental sample from an environmental source selected from rivers, lakes, ponds, oceans, glaciers, icebergs, rain, snow, sewage, reservoirs, tap water, drinking water, etc.; or a group of solid samples from soil, compost, sand, rocks, concrete, wood, bricks, sewage, air, underwater vents, industrial exhaust gas, vehicle exhaust gas, and any combination thereof.

[0345] DC19. The method according to any of the preceding method embodiments, wherein the sample is a food sample selected from the group consisting of: raw materials, cooked foods, plant and animal food sources, pre-treated foods, partially or fully processed foods, and any combination thereof.

[0346] DC20. The method according to any one of the foregoing embodiments, wherein the sample is blood and the biological entity is red blood cells, white blood cells and / or platelets.

[0347] DC21. The method according to implementation scheme DC20 further comprises:

[0348] (f) Calculate the volume of red blood cells, white blood cells and / or platelets based on their respective reconstructed three-dimensional volumes.

[0349] DC22. The method according to implementation scheme DC21 further includes:

[0350] (g) Based on the calculated volume, determine the blood test readings selected from the following groups: mean erythrocyte volume (MCV), hematocrit, erythrocyte distribution width (RDW), mean platelet volume (MPV), platelet distribution width (PDW), immature platelet fraction (IPF), and any combination thereof.

[0351] E. Machine learning-assisted measurement and imaging

[0352] E-1. QMAX device for analysis and imaging

[0353] A device for the detection and localization of bioanalytes is disclosed, comprising a QMAX device, an imager, and a computing unit. A biological sample is prepared for analysis on the QMAX device. This disclosure allows for the acquisition of the count and location of the analytes contained in the sample.

[0354] The imager captures an image of the biological sample. The image is then submitted to a computing unit. The computing unit can be physically connected directly to the imager, via a network connection, or indirectly via image transmission.

[0355] E-2. Workflow

[0356] The disclosed analyte detection and localization employ machine learning and deep learning. Machine learning algorithms are those capable of learning from data. A more rigorous definition of machine learning is: "If the performance of a computer program, measured by P, at a task in T improves with experience E, then the computer program is said to learn from experience E about a class of tasks T and performance measurement P." It explores the research and construction of algorithms capable of learning from and predicting from data. These algorithms overcome the problem of adhering to strictly static program instructions by building models from sample inputs to perform data-driven predictions or decisions.

[0357] Deep learning is a specific type of machine learning based on a set of algorithms that attempt to model high-level abstractions in data. In a simple case, there might be two sets of neurons: one set receives input signals and the other set sends output signals. When an input layer receives input, it passes a modified version of the input to the next layer. In deep networks, there are many layers between the input and output (and these layers are not made up of neurons, but it helps to think in this way), allowing the algorithm to use multiple processing layers consisting of multiple linear and nonlinear transformations.

[0358] The disclosed analyte detection and localization workflow includes two phases: training and prediction, such as... Figure 17A As shown. We will describe the training and prediction phases in the following paragraphs.

[0359] During the training phase, annotated training data is fed into the convolutional neural network. A convolutional neural network is a specialized type of neural network used to process data with a known grid-like topology. Examples include time-series data and image data; time-series data can be considered as a 1D grid sampled at regular time intervals, and image data can be considered as a 2D grid of pixels. Convolutional networks have been very successful in practical applications. The name "convolutional neural network" indicates that the network employs a mathematical operation called convolution. Convolution is a special type of linear operation. Convolutional networks are simple neural networks that use convolution instead of general matrix multiplication in at least one layer.

[0360] Annotate the training data for the analyte to be detected. The annotation indicates whether the analyte exists in the training data. The annotation can be in the form of a bounding box that completely contains the analyte or the center location of the analyte. In the latter case, the center location is further transformed into a circle covering the analyte.

[0361] When training data is large, two challenges arise: annotation (usually done manually) is time-consuming, and training is computationally expensive. To overcome these challenges, the training data can be divided into small patches, and then these patches, or a portion of these patches, can be annotated and used for training.

[0362] Annotated training data is fed into a convolutional neural network for model training. The output is a model that can be used to make pixel-level predictions of images. We use the Caffe library with a fully convolutional network (FCN). Other convolutional neural network architectures, such as TensorFlow, can also be used.

[0363] The training phase generates a model that will be used in the prediction phase. This model can be reused in the prediction phase of the input image. Therefore, the computational unit only needs access to the generated model. It does not need access to the training data, nor does it need to run the training phase on the computational unit.

[0364] predict

[0365] In the prediction phase, a detection component is applied to the input image, followed by a localization component. The output of the prediction phase is the count of analytes contained in the sample and the location of each analyte.

[0366] In the detection component, the input image, along with the model generated from the training phase, is fed into a convolutional neural network. The output of the detection level is a pixel-level prediction in the form of a heatmap. The heatmap can have the same size as the input image, or it can be a scaled-down version of the input image. Each pixel in the heatmap has a value from 0 to 1, which can be considered as the probability (belief) of whether the pixel belongs to the analyte. The higher the value, the greater the chance that it belongs to the analyte.

[0367] The heatmap is the input to the localization component. We disclose an algorithm for locating the center of an object. The main idea is to iteratively detect local peaks from the heatmap. After finding a peak, we calculate the local region around the peak with smaller values. We remove this region from the heatmap and find the next peak from the remaining pixels. This process is repeated until all pixels are removed from the heatmap.

[0368] One implementation of the localization algorithm involves sorting the heatmap values ​​from highest to lowest into a one-dimensional sequential list. The pixel with the highest value is then selected and removed from the list along with its neighboring pixels. This process is repeated to select the pixel with the highest value from the list until all pixels have been removed.

[0369] Global search algorithm (heatmap)

[0370] enter:

[0371] Heatmap

[0372] Output:

[0373]

[0374] After sorting, the heatmap is a one-dimensional sorted list where heatmap values ​​are ordered from highest to lowest. Each heatmap value is associated with its corresponding pixel coordinates. The first item in the heatmap is the item with the highest value, which is the output of the `pop(heatmap)` function. A disk is created with the pixel coordinates of the disk containing the highest heatmap value at its center. Then, all heatmap values ​​whose pixel coordinates are within the disk are removed from the heatmap. This algorithm repeatedly pops the highest value from the current heatmap and removes the disks surrounding it until the item is removed from the heatmap.

[0375] In the sorted list heatmap, each item knows its successors and subsequent items. When an item is removed from the sorted list, we make the following changes, such as... Figure 17B As shown:

[0376] • Assume the item to be deleted is x r Its continuation term is x p Its following term is x f .

[0377] • For the continuation term x p , redefine its follower as the follower of the deleted item. Therefore, x p The following item is the current x f .

[0378] • For the item x to be deleted r If no continuation or follow-up items are defined, then remove them from the sort list.

[0379] • For the following item x f This redefines its continuation as a continuation of the deleted item. Therefore, x f The continuation term is now x p .

[0380] After all items are removed from the sorted list, the localization algorithm is complete. The number of elements in this set of loci will be the count of the analytes, and the location information will be the pixel coordinates per second in this set of loci.

[0381] Another implementation searches for local peaks that are not necessarily the local peak with the highest heatmap value. To detect each local peak, we start from a random starting point and search for local maxima. After finding a peak, we calculate the local region around the peak with smaller values. This region is removed from the heatmap, and the next peak is found from the remaining pixels. This process is repeated until all pixels are removed from the heatmap.

[0382] Local search algorithm (s, heatmap)

[0383] enter:

[0384] s: Starting position (x, y)

[0385] Heatmap

[0386] Output:

[0387] s: Location of the local peak.

[0388] We only consider pixels with values ​​greater than 0.

[0389] Algorithm coverage (s, heatmap)

[0390] enter:

[0391] s: Location of the local peak.

[0392] Heat map:

[0393] Output:

[0394] Coverage: A group of pixels covered by the peak:

[0395] This is a breadth-first search algorithm starting from s, with a conditional access point: only when heatmap[p] > 0 and heatmap[p] <= heatmap[q] is a neighboring p at the current position q added to cover the area. Therefore, each covered pixel has a non-descent path to the local peak s.

[0396] Algorithm localization (heatmap) input:

[0397] Heatmap

[0398] Output:

[0399] loci

[0400] loci←{}

[0401] Pixels ← {All pixels in the heatmap}

[0402] And the pixel is not empty.

[0403] s ← Any pixel from the pixel

[0404] s ← Local search(s, heatmap) / / s is now a local peak

[0405] Probe a local region of radius R around s to obtain better local peak values.

[0406] r ← Coverage(s, heatmap)

[0407] Pixel ← Pixel \r / / Delete all pixels covered

[0408] Add s to loci

[0409] E-3. Embodiments of the Invention

[0410] EA1. A deep learning method for data analysis, comprising:

[0411] (a) Receive an image of a test sample, wherein the sample is loaded into the QMAX device and the image is captured by an imager connected to the QMAX device, wherein the image includes detectable signals from analytes in the test sample;

[0412] (b) Analyze the image using a detection model and generate a 2-D data array of the image, wherein the 2-D data array includes probability data of the analyte at each location in the image, and establish the detection model through a training process, which includes:

[0413] i. Feed the annotated dataset into the convolutional neural network, where the annotated dataset comes from samples of the same type as the test samples and for the same analyte;

[0414] ii. Train and build a detection model through convolution;

[0415] (c) Analyze the 2-D data array using the following steps to detect local signal peaks:

[0416] i. Signal list procedure, or

[0417] ii. Local search process; and

[0418] (d) Calculate the amount of the analyte based on local signal peak information.

[0419] EB1. A system for data analysis, comprising:

[0420] The QMAX device, imager, and computing unit include:

[0421] (a) The QMAX device is configured to compress at least a portion of the test sample into a layer of highly uniform thickness;

[0422] (b) The imager is configured to generate an image of the sample at a layer of uniform thickness, wherein the image includes a detectable signal from an analyte in the test sample;

[0423] (c) The computing unit is configured as follows:

[0424] i. Receive images from the imager;

[0425] ii. Analyze the image using the detection model and generate a 2D data array of the image, where 2D

[0426] The data array includes probability data for the analyte at each location in the image, and is trained...

[0427] The training process establishes the detection model, which includes:

[0428] The annotated dataset is fed into the convolutional neural network, where the annotated dataset comes from...

[0429] Samples of the same type as the test sample and for the same analyte;

[0430] The detection model is trained and built using convolution;

[0431] iii.(c) Using a signal list procedure or a local search procedure to divide the 2-D data array

[0432] Analysis to detect local signal peaks; and

[0433] iv. Calculate the amount of analyte based on local signal peak information.

[0434] EA2. The method according to implementation scheme EA1, wherein signal list processing includes:

[0435] i. Establish a signal list by iteratively detecting local peaks in a two-dimensional data array, calculate the local regions surrounding the detected local peaks, and sequentially remove the detected peaks and local region data from the signal list; and

[0436] ii. Local signal peaks are detected by repeatedly removing the highest signal from the signal list and removing signals around the highest signal.

[0437] EA3. The method according to any one of the implementation schemes EA, wherein the local search procedure comprises:

[0438] i. Search for local maxima in a 2-D data array starting from random points;

[0439] ii. Calculate the local region around the peak but with smaller values;

[0440] iii. Remove local maxima and their surrounding smaller values ​​from a 2-D data array; and

[0441] iv. Repeat steps i-iii to detect local signal peaks.

[0442] EA4. The method according to any of the foregoing implementations of EA, wherein the annotated dataset is partitioned before annotation.

[0443] EB2. The system according to implementation scheme EB1, wherein the imager includes a camera.

[0444] EB3. The system according to implementation scheme EB2, wherein the camera is part of a mobile communication device.

[0445] EB4. The system according to any of the foregoing embodiments EB, wherein the computing unit is part of a mobile communication device.

[0446] F. Apparatus and methods for tissue staining and cell imaging

[0447] F-1. Example of a QMAX device for tissue staining and cell imaging

[0448] Figure 18 Implementations of a general-purpose QMAX device with or without hinges are shown, where Q: quantization; M: amplification; A: reagent addition; X: acceleration; also known as a Compressed Regulation Open Flow (CROF) device. The general-purpose QMAX device includes a first plate 10 and a second plate 20. Specifically, A shows a perspective view of the first plate 10 and the second plate 20, where the first plate has spacers. However, it should be noted that the spacers are also fixed to the second plate 20 (not shown) or both the first plate 10 and the second plate 20 (not shown). B shows a perspective and cross-sectional view of sample 90 deposited on the first plate 10 in an open configuration; however, it should be noted that sample 90 is also deposited on the second plate 20 (not shown), or both the first plate 10 and the second plate 20 (not shown). C shows (i) extending sample 90 using the first plate 10 and the second plate 20 (sample flows between the inner surfaces of the plates) and reducing sample thickness, and (ii) adjusting sample thickness using spacers and plates in a closed configuration of the QMAX device. The inner surface of each plate has one or more binding sites and / or storage sites (not shown).

[0449] In some embodiments, spacer 40 has a predetermined uniform height and a predetermined uniform spacer spacing. Average LOD - 8 ppb. In closed configurations, such as... Figure 1C As shown, the spacing between the plates, and therefore the thickness of the sample 90, is adjusted by the spacer 40. In some embodiments, the uniform thickness of the sample 90 is substantially similar to the uniform height of the spacer 40. It should be noted that, although Figure 18 Figure A shows a spacer 40 to be fixed to one of the plates, but in some embodiments, the spacer is not fixed. For example, in some embodiments, the spacer is mixed with the sample such that when the sample is compressed into a thin layer, the spacer acts as a rigid bead or particle with uniform size to adjust the thickness of the sample layer.

[0450] Figure 18Figure A illustrates an embodiment of a QMAX device for cell imaging. As shown, the device includes a first plate 10, a second plate 20, and spacers 40. The plates are movable relative to each other into different configurations, and one or both plates are flexible. Each plate has a sample contact area (not shown) on its respective inner surface for contacting staining solution 910 and / or tissue sample 90 suspected of containing the target analyte. The second plate 20 includes spacers 40 fixed to its inner surface 21; the spacers 40 have a predetermined substantially uniform height and a predetermined spacer spacing, and at least one spacer is located within the sample contact area.

[0451] Figure 18 Figures A and B illustrate a configuration known as an open configuration. As shown, in an open configuration, the two plates are partially or completely separated, the gap 102 between the plates is not adjusted by the spacer 40, and the staining solution 910 and sample 90 are deposited on the first plate 10. It should be noted that the staining solution 910 and sample 90 may also be deposited on the second plate 20 or both plates.

[0452] Figure 18 Figures A and C illustrate an alternative configuration of the two plates: a closed configuration. As shown in Figure B, a closed configuration is constructed after the staining solution 910 and sample 90 are deposited in an open configuration. In this closed configuration, at least a portion of sample 90 is between the two plates, and a layer of at least a portion of staining solution 910 is between at least a portion of sample 90 and the second plate 20. The thickness of this staining solution layer is at least a portion adjusted by the plates, sample 90, and spacer 40, and the average distance between the sample surface and the surface of the second plate is equal to or less than 250 μm, with minimal variation.

[0453] In some embodiments, the sample may be dried in an open configuration thereon, and the sample contains a body fluid selected from: amniotic fluid, aqueous humor, vitreous fluid, blood (e.g., whole blood, graded blood, plasma, or serum), breast milk, cerebrospinal fluid (CSF), earwax, chyle, chyme, endolymph, perilymph, feces, respiration, gastric acid, gastric juice, lymph, mucus (including nasal drainage and sputum), pericardial fluid, peritoneal fluid, pleural fluid, pus, rheumatism, saliva, exhaled respiratory condensate, sebum, sebum, sputum, sweat, synovial fluid, tears, vomitus, urine, and any combination thereof.

[0454] In some embodiments, the sample contact areas of these one or two plates are configured such that the sample can be dried on them in an open configuration, and the sample contains a blood smear and is dried on one or two plates.

[0455] In some embodiments, the sample is a solid tissue section with a thickness of 1-200 μm, and the sample contact area of ​​one or two plates is adhered to the sample. In some embodiments, the sample is paraffin-embedded. In some embodiments, the sample is blood.

[0456] In some embodiments, the staining solution is a pure buffer solution that does not specifically contain components capable of altering the properties of the sample. In some embodiments, the staining solution contains a fixative capable of fixing the sample. In some embodiments, the staining solution contains a blocking agent configured to prevent non-specific endogenous species in the sample from reacting with a detection agent used to specifically label the target analyte. In some embodiments, the staining solution contains a dewaxing agent capable of removing paraffin from the sample. In some embodiments, the staining solution contains a permeabilizing agent capable of permeating cells in a tissue sample containing the target analyte. In some embodiments, the staining solution contains an antigen retrieval agent capable of promoting antigen retrieval. In some embodiments, the staining solution contains a detection agent that specifically labels the target analyte in the sample. In some embodiments, the sample contact area of ​​one or both plates includes a storage site containing a capping agent configured to prevent non-specific endogenous species in the sample from reacting with a detection agent used to specifically label the target analyte. In some embodiments, the sample contact area of ​​one or both plates includes a storage site containing a dewaxing agent capable of removing paraffin from the sample. In some embodiments, the sample contact area of ​​one or both plates includes a storage site containing a permeabilizing agent capable of permeating cells in a tissue sample containing a target analyte. In some embodiments, the sample contact area of ​​one or both plates includes a storage site containing an antigen retrieval agent capable of promoting antigen retrieval. In some embodiments, the sample contact area of ​​one or both plates includes a storage site containing a detection reagent that specifically labels the target analyte in the sample. In some embodiments, the sample contact area of ​​one or both plates includes a binding site containing a trapping agent configured to bind to the target analyte on the surface of cells in the sample and immobilize the cells.

[0457] In some implementations, the detection reagent includes a staining agent selected from the group consisting of: Acid Fuchsin, Alcian Blue 8GX, Alizarin Red S, Aniline Blue WS, Basic Yellow O, Azo Carmine B, Azo Carmine G, Azure A, Azure B, Azure C, Basic Fuchsin, Bismarck Brown Y, Brilliant Cresol Blue, Brilliant Green, Carmine, Chloramphenicol Black E, Congo Red, C1 Cresol Violet, Crystal Violet, Dassard Red, Eosin B, Eosin Y, Erysipelothrix, Ethyl Eosin, Ethyl Green, Fast Green FCF, Fluorescein Isothiocyanate, Giemsa stain, Hematoxylin, Hematoxylin and Eosin, indigo carmine, Janus Green B, Janus Green 1899, light green SF, malachite green, Matthew Yellow, methyl orange, methyl violet 2B, methylene blue, methylene blue, methylene violet, (methylene blue), neutral red, aniline black, Nile blue A, nucleoside red, oil red, orange G, orange II, lichen red, pararosaniline, pararosaniline, pararosaniline, pyrrolizin B, pyrrolizin, azurite, rose red, safranin O, Sudan Black B, Sudan III, Sudan V, tetrachromium stain, thionine, toluidine blue, Wiggert, Wright stain, and any combination thereof.

[0458] In some implementations, the detection reagent contains antibodies configured to specifically bind to protein analytes in the sample.

[0459] In some implementations, the detection agent comprises an oligonucleotide probe configured to specifically bind to DNA and / or RNA in the sample.

[0460] In some implementations, the detection reagent is labeled with a reporter molecule, which is configured to provide a detectable signal to be read and analyzed.

[0461] In some embodiments, the signal is selected from the group consisting of:

[0462] i. Light emission selected from photoluminescence, electroluminescence, and electrochemiluminescence;

[0463] ii. Light absorption, reflection, transmission, diffraction, scattering, or diffusion;

[0464] iii. Surface Raman scattering;

[0465] iv. Resistive reactance selected from resistors, capacitors, and inductors;

[0466] v. Magnetic relaxation;

[0467] vi. and any combination of iv.

[0468] F-2. Immunohistochemistry

[0469] In some embodiments, the apparatus and method of the present invention can be used for immunohistochemistry of samples.

[0470] In immunohistochemical (IHC) staining, tissue samples are fixed (e.g., in paraformaldehyde), optionally embedded in paraffin, cut into thin sections less than 100 μm thick (e.g., 2 μm to 6 μm thick), and then fixed onto a support such as a glass slide. Once fixed, the tissue sections can be dehydrated using an alcohol wash with increased concentration and clarified using a detergent such as xylene.

[0471] In most IHC methods, both first and second antibodies can be used. In these methods, the first antibody binds to the antigen of interest (e.g., a biomarker) and is unlabeled. The second antibody binds to the first antibody and is conjugated directly to a reporter molecule or a linker molecule (e.g., biotin) that can collect the reporter molecule in solution. Alternatively, the first antibody itself may be conjugated directly to a reporter molecule or a linker molecule (e.g., biotin) that can collect the reporter molecule in solution. Reporter molecules include fluorophores (e.g., FITC, TRITC, AMCA, luciferin, and rhodamine) and enzymes such as alkaline phosphatase (AP) and horseradish peroxidase (HRP), with various fluorescent, chromogenic, and chemiluminescent substrates such as DAB or BCIP / NBT.

[0472] In the direct method, tissue sections are incubated with a labeled primary antibody (e.g., a FITC-conjugated antibody) in a binding buffer. The primary antibody binds directly to the antigen in the tissue section, and the section is analyzed under a microscope after washing to remove any unbound primary antibody.

[0473] In the indirect method, tissue sections are incubated with unlabeled primary antibodies that bind to the target antigen in the tissue. After washing the tissue sections to remove the unbound primary antibody, the tissue sections are incubated with labeled secondary antibodies that bind to the primary antibody.

[0474] After immunohistochemical staining of the antigen, tissue samples can be stained with another staining agent, such as hematoxylin, Hoechst stain, and DAPI, to provide contrast and / or identify other features.

[0475] This device can be used for immunohistochemical (IHC) staining of tissue samples. In these embodiments, the device may include a first plate and a second plate, wherein: the plates can be moved relative to each other in different configurations; one or both plates are flexible; each plate has a sample contact area on its respective surface for contacting the tissue sample or IHC staining solution; the sample contact area in the first plate is smooth and flat; the sample contact area in the second plate includes spacers fixed to the surface and having a predetermined substantially uniform height and a predetermined constant spacer spacing in the range of 7 μm to 200 μm;

[0476] One of these configurations is an open configuration, wherein the two plates are completely or partially separated and the spacing between the plates is not adjustable by the spacers; and another of this configuration is a closed configuration, which is constructed after the sample and IHC staining solution are deposited in an open configuration; and in the closed configuration, at least a portion of the sample is between the two plates and at least a portion of the sample is separated from the second plate by a layer of staining solution, wherein at least a portion of the thickness of the staining solution layer is adjustable by the plates, the sample and the spacers, and the average distance between the sample surface and the surface of the second plate is equal to or less than 250 μm and varies very little.

[0477] In some embodiments, the apparatus may include a dried IHC staining agent coated on the sample contact area of ​​one or both plates. In some embodiments, the apparatus may include a dried IHC staining agent coated on the sample contact area of ​​a second plate, and the IHC staining solution contains a liquid dissolving the dried IHC staining agent. The apparatus of claim 1, wherein the sample thickness is 2 μm to 6 μm.

[0478] F-3.H&E and special staining

[0479] In some embodiments, the apparatus and method of the present invention can be used for H&E staining and special staining.

[0480] Hematoxylin and eosin staining, or hematoxylin and eosin staining (H&E staining or HE staining), is one of the primary staining methods in histology. It is the most widely used staining agent in medical diagnosis and is often considered the gold standard; for example, when pathologists examine biopsies of suspected cancerous tissue, the histological sections may be stained with H&E and referred to as "H&E sections," "H+E sections," or "HE sections." The combination of hematoxylin and eosin produces blue, violet, and red stains.

[0481] In diagnostic pathology, the term "special staining" is most commonly used in a clinical setting and refers simply to any technique other than hematoxylin and eosin (H&E) staining used to color a sample. This also includes immunohistochemistry and in situ hybridization staining. H&E staining, on the other hand, is the most commonly used staining method in histological and medical diagnostic laboratories.

[0482] In any embodiment, the dry binding site may comprise a trapping agent, such as an antibody or nucleic acid. In some embodiments, the releasable drying agent may be a labeled agent, such as a fluorescently labeled agent, like a fluorescently labeled antibody or a cell staining agent, such as Romanovsky stain, Ressmann stain, McGlinwa stain, Giemsa stain, Zener's stain, Wright's stain, or any combination thereof (e.g., a mixture of Ressmann and Giemsa stains). Such a staining agent may contain eosin Y or eosin B containing methylene blue. In some embodiments, the staining agent may be a basic staining agent, such as hematoxylin.

[0483] In some implementations, the special staining agents include, but are not limited to, Acid Fuchsin, Alcian Blue 8GX, Alizarin Red S, Aniline Blue WS, Basic Yellow O, Azo Carmine B, Azo Carmine G, Azure A, Azure B, Azure C, Basic Fuchsin, Bismarck Brown Y, Brilliant Cresol Blue, Brilliant Green, Carmine, Chloramphenicol Black E, Congo Red, C1 Cresol Violet, Crystal Violet, Dassard Red, Eosin B, Eosin Y, Erysipelothrix, Ethyl Eosin, Ethyl Green, Fast Green FCF, Fluorescein Isothiocyanate, Giemsa stain, Hematoxylin, Hematoxylin and Eosin, Indigo Carmine, Janus Green B, Janus 1899, Pale Green SF, Malachite Green, Masseus Yellow, Methyl Orange, Methyl Violet 2B, Methylene Blue, Methylene Blue, Methylene Violet, (Methylene Blue), Neutral Red, Aniline Black, Nile Blue A, Nucleotide Red, Oil Red, Orange G, Orange II, Lichen Red, Pararosaniline, Pararosaniline, Pararosaniline, Pyrrocin B, Pyrrocin, Rezazon, Rose Red, Safranin O, Sudan Black B, Sudan III, Sudan V, Tetrachromium Stain, Thionium, Toluidine Blue, Wiggert, Wright Stain, and any combination thereof.

[0484] F-4. In situ hybridization technology

[0485] In some embodiments, the apparatus and method of the present invention can be used to perform in situ hybridization (ISH) on tissue samples.

[0486] In situ hybridization (ISH) is a type of hybridization that uses labeled complementary DNA, RNA, or modified nucleic acid strands (i.e., probes) to localize a specific DNA or RNA sequence in a part or portion of a tissue (in situ), or, if the tissue is small enough (e.g., plant seeds, fruit fly embryos), to the entire tissue (integrated ISH), cells, and circulating tumor cells (CTCs).

[0487] In situ hybridization (ISH) is used to reveal the location of specific nucleic acid sequences on chromosomes or in tissues, a crucial step in understanding gene organization, regulation, and function. Key techniques currently in use include: in situ hybridization with mRNA using oligonucleotides and RNA probes (radiolabeled and hapten-labeled); analysis using light and electron microscopy; whole-cell in situ hybridization; dual detection of RNA and RNA plus protein; and fluorescence in situ hybridization (FISH) for detecting chromosome sequences. DNA ISH can be used to determine chromosome structure. Fluorescent DNA ISH (FISH) can be used, for example, in medical diagnostics to assess chromosome integrity. RNA ISH (RNA in situ hybridization) is used to measure and locate RNA (mRNA, lncRNA, and miRNA) within tissue sections, cells, whole-cell scaffolds, and circulating tumor cells (CTCs).

[0488] In some implementations, the detection reagent comprises nucleic acid probes for in situ hybridization staining. Nucleic acid probes include, but are not limited to, oligonucleotide probes configured to specifically bind to DNA and / or RNA in a sample.

[0489] F-5. Systems and methods for tissue staining and cell imaging

[0490] A system for rapid staining and analysis of tissue samples using a mobile phone is also provided, comprising:

[0491] (a) The sample, staining solution, and apparatus as described above.

[0492] (b) Mobile Communications

[0493] An apparatus comprising:

[0494] i. One or more cameras used to detect and / or image a sample;

[0495] ii. Electronic devices, signal processors, hardware, and software for receiving and / or processing detected signals and / or images of samples and for remote communication;

[0496] (c) A light source from a mobile communication device or an external source.

[0497] A method for rapid staining and analysis of tissue samples using a mobile phone is also provided, comprising:

[0498] (a) Deposit tissue samples and staining solutions onto the apparatus of the above system and place the two plates in a closed configuration;

[0499] (b) Acquiring a mobile phone with hardware and software for imaging, data processing and communication;

[0500] (c) Determination of tissue samples deposited on a CROF device via mobile phone to produce results; and

[0501] (d) Transmit the results from the mobile phone to a location far from the mobile phone.

[0502] A method for staining tissue samples is also provided, comprising:

[0503] (a) Obtaining tissue samples;

[0504] (b) Obtain the staining solution;

[0505] (c) The first board and the second board, wherein:

[0506] The plates can be moved relative to each other to form different configurations;

[0507] One or two of the plates are flexible;

[0508] Each plate has a sample contact area on its respective surface for contacting tissue samples or IHC staining solution;

[0509] The sample contact area in the first plate is smooth and flat;

[0510] The sample contact area in the second plate includes spacers fixed to the surface and having a predetermined substantially uniform height and a predetermined constant spacer spacing, the spacer spacing being in the range of 7 μm to 200 μm.

[0511] (c) Depositing a sample on one or two plates; when the plates are configured in an open configuration, wherein the open configuration is a configuration in which two plates are partially or completely separated and the spacing between the plates is not adjusted by spacers;

[0512] (d) After (c), at least a portion of the tissue sample and at least a portion of the staining solution are compressed into a closed structure using two plates;

[0513] In this closed structure: at least a portion of the sample is between the two plates and at least a portion of the staining solution layer is between at least a portion of the sample and the second plate, wherein at least a portion of the staining solution layer is adjusted by the plates, the sample and the spacer, and the average distance between the sample surface and the surface of the second plate is equal to or less than 250 μm, with very little variation.

[0514] All the benefits and advantages described in other embodiments (e.g., accelerated response, faster results, etc.) can be applied to the apparatus, system, and method.

[0515] Furthermore, all parameters described above in the context of other embodiments (e.g., the size, spacing, and shape of the spacers, the flexibility of the spacers and plates, and how the devices and systems can be used, etc.) can be incorporated into the IHC implementation described in this section.

[0516] For example, in some embodiments, the spacers of the uniformly thick layer (i.e., spacers that separate the plates from each other in the layer) have a “fill factor” of at least 1%, for example, at least 2% or at least 5%, where the fill factor is the ratio of the area of ​​the spacers in contact with the uniformly thick layer to the total area of ​​the plates in contact with the uniformly thick layer. In some embodiments, for the spacers of the uniformly thick layer, the Young's modulus of the spacers multiplied by the fill factor of the spacers is equal to or greater than 10 MPa, for example, at least 15 MPa or at least 20 MPa, where the fill factor is the ratio of the area of ​​the spacers in contact with the uniformly thick layer to the total area of ​​the plates in contact with the uniformly thick layer. In some embodiments, the thickness of the flexible plate multiplied by the Young's modulus of the flexible plate is in the range of 60 to 300 GPaμm. In some embodiments, for the flexible plate, the fourth power of the spacer spacing (ISD) divided by the thickness (h) of the flexible plate and the Young's modulus (E) of the flexible plate, ISD 4 / (ΔE) is equal to or less than 10 6 μm 3 / GPa, for example, less than 10 5 μm 3 / Gpa, less than 10 4 μm 3 / GPa or less than 10 3 μm 3 / GPa.

[0517] In some embodiments, one or both plates include location markings on or within the plates that provide information about the plate's location, such as the location to be analyzed or the location where a segment should be deposited. In some cases, one or both plates may include scale markings on or within the plates that provide information about the lateral dimensions of the segment and / or plate structure. In some embodiments, one or both plates include imaging markings on or within the plates that facilitate the imaging of the sample. For example, imaging markings can help focus an imaging device or guide the imaging device to a position on the device. In some embodiments, spacers can be used as location markings, scale markings, imaging markings, or any combination thereof.

[0518] In some embodiments, the spacing between spacers can be substantially periodic. In some cases, the spacers can be in a regular pattern and the spacing between adjacent spacers can be substantially the same. In some embodiments, the spacers are columns having a cross-sectional shape selected from circles, polygons, circles, squares, rectangles, ellipses, or any combination thereof, and in some embodiments, the spacers can have a generally flat top surface, wherein for each spacer, the ratio of its lateral dimension to its height is at least 1. In some embodiments, the minimum lateral dimension of the spacer is less than or substantially equal to the minimum size of the analyte in the fluid sample. The minimum lateral dimension of the spacers is in the range of 0.5 μm to 100 μm, for example, in the range of 2 μm to 50 μm or 0.5 μm to 10 μm.

[0519] In some embodiments, the spacer has a cylindrical shape, and the sidewall corners of the spacer have a circular shape with a radius of curvature of at least 1 μm, such as at least 1.2 μm, at least 1.5 μm, or at least 2.0 μm. The spacer can have any convenient density, such as at least 1000 / mm². 2 Density, for example, at least 1000 / mm 2 Density, at least 2000 / mm 2 Density, at least 5,000 / mm 2 Density or at least 10,000 / mm 2 The density.

[0520] In this device, at least one plate can be transparent, thereby allowing optical readout measurements. Similarly, in this device, at least one plate can be made of a flexible polymer, thereby allowing the sample to be efficiently deployed by compressing the plates together. In some embodiments, the spacers are incompressible for the pressure required to compress these plates and / or independently, only one of these plates is flexible. The flexible plates can have a thickness ranging from 20 μm to 200 μm, for example, in the range of 50 μm to 150 μm. As mentioned above, in the closed position, the thickness of the uniform thickness layer can have small variations.

[0521] In some implementations, the change can be less than 10%, less than 5%, or less than 2%, which means that the thickness of the region does not exceed + / - 10%, + / - 5%, or + / - 2% of the average thickness.

[0522] In some embodiments, the first and second plates are connected, and the device can be changed from an open configuration to a closed configuration by folding the plates. In some embodiments, the first and second plates are connected by a hinge, and the device can be changed from an open configuration to a closed configuration by folding the plates so that the device bends along the hinge. The hinge may be a separate material attached to the plates, or in some cases, the plates may be integrally formed with the plates.

[0523] In some implementations, the device is capable of analyzing the portion very quickly. In some cases, analysis can be performed in 60 seconds or less, 30 seconds, 20 seconds, 15 seconds, or 10 seconds or less.

[0524] In some embodiments, the system may additionally include (d) a housing configured to hold the sample and mount it to the mobile communication device. The housing may contain optics for facilitating imaging and / or signal processing of the sample by the mobile communication device, and a base configured to hold the optics on the mobile communication device. In some cases, the optical elements of the device (e.g., lenses, filters, mirrors, prisms, or beam splitters) may be movable, allowing the sample to be imaged in at least two channels.

[0525] In some implementations, the mobile communication device can be configured to transmit test results to medical personnel (e.g., MDs), healthcare institutions (e.g., hospitals or testing laboratories), or insurance companies. Furthermore, the mobile communication device can be configured to communicate information about the subject (e.g., the subject's age, sex, weight, address, name, previous test results, previous medical history, etc.) with medical professionals, healthcare institutions, or insurance companies. In some implementations, the mobile communication device can be configured to receive prescriptions, diagnoses, or recommendations from medical personnel. For example, in some implementations, the mobile communication device can send laboratory results to a remote location where a medical personnel provide a diagnosis. Diagnoses can be transmitted to the subject via the mobile communication device.

[0526] In some implementations, the mobile communication device may include hardware and software that allows it to (a) capture images of a sample; (b) analyze test and control locations in the images; and (c) compare values ​​obtained from the analysis of the test locations with thresholds characterizing rapid diagnostic tests. In some cases, the mobile communication device communicates with remote locations via wireless or cellular networks.

[0527] In any embodiment, the mobile communication device may be a mobile phone.

[0528] This system can be used in a method comprising (a) taking a sample on a device of the system; (b) measuring the sample deposited on the device to produce results; and (c) transmitting the results from a mobile communication device to a location remote from the mobile communication device. The method may include analyzing the results at a remote location to provide analytical results; and transmitting the analytical results from the remote location to the mobile communication device. As described above, the analysis can be performed by a medical professional at the remote location. Furthermore, in some embodiments, the mobile communication device can receive prescriptions, diagnoses, or recommendations from a medical professional at the remote location.

[0529] A method for analyzing tissue sections is also provided. In some embodiments, the method may include obtaining the apparatus as described above, depositing the portion onto one or both plates of the apparatus; placing the plates in a closed configuration and applying external force to at least a portion of the plates; and analyzing a sample in a uniform thickness layer when the plates are in a closed configuration.

[0530] In some embodiments, the device includes:

[0531] (a) Obtaining tissue sections;

[0532] (b) Obtaining a first plate and a second plate movable relative to each other in different configurations, wherein each plate has a substantially flat sample contact surface, one or both plates are flexible, and said one or both plates include spacers fixed to the respective sample contact surfaces, and said spacers have:

[0533] i. A predetermined, substantially uniform height.

[0534] ii. The shape of a column having a substantially uniform cross-section and a flat top surface;

[0535] iii. The ratio of width to height is equal to or greater than 1;

[0536] iv. A predetermined constant interval distance in the range of 10 μm to 200 μm;

[0537] v. The fill factor is equal to or greater than 1%;

[0538] (c) Depositing a sample on one or two plates; when the plates are configured in an open configuration, wherein the open configuration is a configuration in which two plates are partially or completely separated and the spacing between the plates is not adjusted by spacers;

[0539] (d) and (c) thereafter, the two plates are used to compress at least a portion of the segment into a layer of substantially uniform thickness, which is constrained by the sample contact surfaces of the plates, wherein the uniform thickness of the layer is adjusted by the spacers and the plates, and has an average value varying by less than 10% in the range of 1.8 μm to 3 μm, wherein the compression comprises:

[0540] Place the two boards together; and

[0541] A region of at least one of these plates is conformally pressed in parallel or sequentially to press the plates together into a closed configuration, wherein the conformal pressing on the plates produces substantially uniform pressure on at least a portion of the sample, and the pressing causes at least a portion of the sample to laterally unfold between the sample contact surfaces of the plates, and wherein the closed configuration is a configuration in which the spacing between the plates in a uniform thickness region layer is adjusted by the spacers.

[0542] (e) Analyze the cross-section in a uniform thickness layer when the plate is closed.

[0543] structure;

[0544] The fill factor is the ratio of the contact area of ​​the spacer to the total plate area;

[0545] Conformal pressing is a method that keeps the pressure applied to a region substantially constant and independent of changes in the shape of the outer surface of the plate; and

[0546] The parallel presses simultaneously apply pressure to the target area, while the sequential presses apply pressure to a portion of the target area and gradually move to other areas.

[0547] In some embodiments, the method may include: removing external forces after the plates are in a closed configuration; and imaging portions of a uniformly thick layer while the plates are in a closed configuration. As described above, in these embodiments, the spacer spacing may be in the range of 20 μm to 200 μm or 5 μm to 20 μm. In these embodiments, the product of the fill factor and the Young's modulus of the spacer is 2 MPa or greater. In some embodiments, the surface variation is less than 30 nm.

[0548] In any of these embodiments, imaging and counting can be accomplished by the following steps: i. irradiating a cross section in a uniformly thick layer; ii. capturing one or more images of the section using a CCD or CMOS sensor.

[0549] In some implementations, the external force may be provided by a person's hand, for example, by pressing down with a finger such as the thumb, or by clamping between the thumb and another finger such as the index finger on the same hand.

[0550] In some embodiments, one or more plates may contain a drying reagent (e.g., a binder, staining agent, detection agent, or assay reactant) coated on one or two plates.

[0551] In some implementations, the thickness uniformity of the uniform thickness sample layer may be at most + / - 5%, for example, at most + / - 2% or at most + / - 1%.

[0552] In some implementations, the spacer is a column with a cross-sectional shape selected from circular, polygonal, annular, square, rectangular, oval, elliptical, or any combination thereof.

[0553] F-6. Embodiments of the Invention

[0554] FA1. An apparatus for analyzing tissue samples, comprising:

[0555] The first plate, the second plate, and the spacer, wherein:

[0556] i. The plates can be moved relative to each other to form different configurations;

[0557] ii. One or both plates are flexible;

[0558] iii. Each plate has a sample contact area on its respective inner surface for contact with staining solution and / or tissue samples suspected of containing the target analyte;

[0559] iv. One or two plates include spacers fixed to the respective plates;

[0560] v. The spacers have a predetermined substantially uniform height and a predetermined spacer spacing, and

[0561] vi. At least one spacer is located inside the sample contact area;

[0562] One of these structures is an open structure, in which the two plates are partially or completely separated, the spacing between the plates is not adjustable by the spacers, and the sample is deposited on one or both of these plates.

[0563] Another configuration is a closed configuration, which is configured to be in an open configuration and a closed configuration after the staining solution and sample are deposited: at least a portion of the sample is between the two plates, and at least a portion of the staining solution layer is between the two plates, at least part of the sample and the second plate, wherein the thickness of the at least part of the staining solution layer is adjusted by the plates, the sample and the spacer, and the average distance between the sample surface and the surface of the second plate is equal to or less than 250 μm with little variation.

[0564] FAA1. An apparatus for analyzing tissue samples, comprising:

[0565] The first plate, the second plate, and the spacer, wherein:

[0566] i. The plates can be moved relative to each other to form different configurations;

[0567] ii.ii. One or both plates are flexible;

[0568] iii. Each plate has a sample contact area on its respective inner surface for contacting the transfer solution and / or tissue samples suspected of containing the target analyte;

[0569] iv. One or two plates contain a staining agent that is dried on the respective sample contact area and is configured to dissolve in the transfer solution upon contact with the transfer solution and stain the tissue sample;

[0570] v. One or two plates include spacers fixed to the respective plates;

[0571] vi. The spacers have a predetermined substantially uniform height and a predetermined spacer spacing, and

[0572] vii. At least one spacer is located inside the sample contact area;

[0573] One of these structures is an open structure, in which the two plates are partially or completely separated, the spacing between the plates is not adjustable by the spacers, and the sample is deposited on one or both of these plates.

[0574] Another of the aforementioned configurations is a closed configuration, which is constructed in the open configuration after the staining solution and the sample are deposited, and in the closed configuration: at least a portion of the sample is between the two plates, and at least a portion of the transfer solution layer is between at least a portion of the sample and the second plate, wherein the thickness of at least a portion of the transfer solution layer is adjusted by the plates, the sample and the spacer, and the average distance between the sample surface and the surface of the second plate is equal to or less than 250 μm, with very little variation.

[0575] FB1. A method for analyzing tissue samples, comprising the following steps:

[0576] (a) Obtain tissue samples suspected of containing the target analyte and staining solution;

[0577] (b) Obtain the first plate, the second plate, and the spacer, wherein:

[0578] i. The plates can be moved relative to each other to form different configurations;

[0579] ii. One or both plates are flexible;

[0580] iii. Each plate has a sample contact area on its respective inner surface for contact with staining solution and / or tissue sample;

[0581] iv. One or two plates include spacers fixed to the respective plates;

[0582] v. The spacers have a predetermined substantially uniform height and a predetermined spacer spacing, and

[0583] vi. At least one spacer is located inside the sample contact area;

[0584] (c) When the plate is in an open configuration, the staining solution and tissue sample are deposited on one or two plates.

[0585] An open structure is a structure in which two plates are partially or completely separated, the spacing between the two plates is not adjustable by spacers, and the sample and staining solution are deposited on one or both plates;

[0586] (d) After (c), the two plates are joined together and pressed into a closed structure.

[0587] The pressing includes pressing a region of at least one of the plates in parallel or sequentially to press the plates together to form a closed structure, wherein the conformal pressing generates substantially uniform pressure on the plates above at least a portion of the sample, and the pressing causes at least a portion of the sample to spread laterally between the inner surfaces of the plates.

[0588] Another part of this structure is a closed structure, which is constructed in the open structure after the staining solution and the sample are deposited, and in the closed structure: at least a portion of the sample is between the two plates and at least a portion of the staining solution layer is between the two plates, at least part of the sample and the second plate, wherein the thickness of the at least part of the staining solution layer is adjusted by the plates, the sample and the spacer, and the average distance between the sample surface and the surface of the second plate is equal to or less than 250 μm with little variation;

[0589] as well as

[0590] (e) Analyze the target analyte when the plate is in a closed configuration.

[0591] FBB1. A method for analyzing tissue samples, comprising the following steps:

[0592] (a) Obtain tissue samples suspected of containing the target analyte and transfer solution;

[0593] (b) Obtain the first plate, the second plate, and the spacer, wherein:

[0594] i. The plates can be moved relative to each other to form different configurations;

[0595] ii. One or both plates are flexible;

[0596] iii. Each plate has a sample contact area on its respective inner surface for contact with staining solution and / or tissue samples suspected of containing the target analyte;

[0597] iv. One or two plates contain a staining agent that is applied to the respective sample contact area and is configured to dissolve in the transfer solution upon contact and stain the tissue sample;

[0598] v. One or two plates include spacers fixed to the respective plates;

[0599] vi. The spacers have a predetermined substantially uniform height and a predetermined spacer spacing, and

[0600] vii. At least one spacer is located inside the sample contact area;

[0601] (c) When the plate is in an open configuration, the staining solution and tissue sample are deposited on one or two plates.

[0602] An open structure is a structure in which two plates are partially or completely separated, the spacing between the two plates is not adjustable by spacers, and the sample and staining solution are deposited on one or both plates;

[0603] (d) After (c), the two plates are joined together and pressed into a closed structure.

[0604] The pressing includes pressing a region of at least one of the plates in parallel or sequentially to press the plates together to form a closed structure, wherein the conformal pressing generates substantially uniform pressure on the plates above at least a portion of the sample, and the pressing causes at least a portion of the sample to spread laterally between the inner surfaces of the plates.

[0605] Another part of this structure is a closed structure, which is constructed in the open structure after the staining solution and the sample are deposited, and in the closed structure: at least a portion of the sample is between the two plates and at least a portion of the staining solution layer is between the two plates, at least part of the sample and the second plate, wherein the thickness of the at least part of the staining solution layer is adjusted by the plates, the sample and the spacer, and the average distance between the sample surface and the surface of the second plate is equal to or less than 250 μm with little variation;

[0606] as well as

[0607] (e) Analyze the target analyte when the plate is in a closed configuration.

[0608] FA2. In some embodiments, the sample may be dried thereon in an open configuration, and wherein the sample comprises a body fluid selected from: amniotic fluid, aqueous humor, vitreous fluid, blood (e.g., whole blood, graded blood, plasma, or serum), breast milk, cerebrospinal fluid (CSF), earwax, chyle, chyme, endolymph, perilymph, feces, respiration, gastric acid, gastric juice, lymph, mucus (including nasal drainage and sputum), pericardial fluid, peritoneal fluid, pleural fluid, pus, rheumatism, saliva, exhaled respiratory condensate, sebum, semen, sputum, sweat, synovial fluid, tears, vomitus, urine, and any combination thereof.

[0609] FAA2. The apparatus according to any of the foregoing embodiments, wherein the dyeing solution has a viscosity in the range of 0.1 mPa·s to 3.5 mPa·s.

[0610] FA3. The apparatus according to any of the foregoing embodiments, wherein the sample contact area of ​​the one or two plates is configured such that the sample can be dried thereon under the open configuration, and wherein the sample comprises a blood smear and is dried on one or two plates.

[0611] FA4. The apparatus according to any of the foregoing embodiments, wherein the sample contact area of ​​one or both plates adheres to the sample, and wherein the sample is a tissue segment with a thickness in the range of 1-200 μm.

[0612] FA5. The apparatus according to embodiment FA4, wherein the sample is embedded in paraffin.

[0613] FA6. The apparatus according to any of the foregoing embodiments, wherein the sample is fixed.

[0614] FA7. The apparatus according to any of the foregoing embodiments, wherein the staining solution contains a fixative capable of fixing the sample.

[0615] FA8. The apparatus according to any of the foregoing embodiments, wherein the staining solution contains a blocking agent, wherein the blocking agent is configured to prevent nonspecific endogenous species in the sample from reacting with a detection agent used to specifically label the target analyte.

[0616] FA9. The apparatus according to any of the foregoing embodiments, wherein the staining solution contains a deparaffinizing agent capable of removing paraffin from the sample.

[0617] FA10. The apparatus according to any of the foregoing embodiments, wherein the staining solution contains a permeation reagent capable of permeating cells in a tissue sample containing the target analyte.

[0618] FA11. The apparatus according to any of the foregoing embodiments, wherein the staining solution contains an antigen retrieval agent capable of promoting antigen retrieval.

[0619] FA12. The apparatus according to any of the foregoing embodiments, wherein the staining solution contains a detection agent that specifically labels the target analyte in the sample.

[0620] FA13. The apparatus according to any of the foregoing embodiments, wherein the sample contact area of ​​one or both plates includes a storage location containing a sealing agent, wherein the sealing agent is configured to prevent non-specific endogenous species in the sample from reacting with the detection agent used to specifically label the target analyte.

[0621] FA14. The apparatus according to any of the foregoing embodiments, wherein the sample contact area of ​​one or both plates includes a storage location containing a dewaxing agent capable of removing paraffin from the sample.

[0622] FA15. The apparatus according to any of the foregoing embodiments, wherein the sample contact area of ​​one or both plates includes a storage site containing a permeation agent capable of permeating cells in a tissue sample containing a target analyte.

[0623] FA16. The apparatus according to any of the foregoing embodiments, wherein the sample contact area of ​​one or both plates includes a storage site containing an antigen retrieval agent capable of promoting antigen retrieval.

[0624] FA17. The apparatus according to any of the foregoing embodiments, wherein the sample contact area of ​​one or both plates includes a storage location containing a detection agent that specifically labels the target analyte in the sample.

[0625] FA18. The apparatus according to any of the foregoing embodiments, wherein the detection reagent comprises a staining agent selected from the group consisting of: Acid Fuchsin, Alcian Blue 8GX, Alizarin Red S, Aniline Blue WS, Basic Yellow O, Azo Carmine B, Azo Carmine G, Azure A, Azure B, Azure C, Basic Fuchsin, Bismarck Brown Y, Brilliant Cresol Blue, Brilliant Green, Carmine, Chloramphenicol Black E, Congo Red, C1 Cresol Violet, Crystal Violet, Dassard Red, Eosin B, Eosin Y, Erysipelothrix, Ethyl Eosin, Ethyl Green, Fast Green FCF, Fluorescein Isothiocyanate, Giemsa stain, Hematoxylin, Hematoxylin and eosin, indigo carmine, Janus Green B, Janus Green 1899, light green SF, malachite green, Matthew Yellow, methyl orange, methyl violet 2B, methylene blue, methylene blue, methylene violet, (methylene blue), neutral red, aniline black, Nile blue A, nucleoside red, oil red, orange G, orange II, lichen red, pararosaniline, pararosaniline, pararosaniline, pyrrolizin B, pyrrolizin, azurite, rose red, safranin O, Sudan Black B, Sudan III, Sudan V, tetrachromium stain, thionine, toluidine blue, Wiggert, Wright stain, and any combination thereof.

[0626] FA19. The apparatus according to any of the foregoing embodiments, wherein the detection reagent comprises an antibody configured to specifically bind to a protein analyte in a sample.

[0627] FA20. The apparatus according to any of the foregoing embodiments, wherein the detection agent comprises an oligonucleotide probe configured to specifically bind to DNA and / or RNA in a sample.

[0628] FA21. The apparatus according to any of the foregoing embodiments, wherein the detector is labeled with a reporter molecule, wherein the reporter molecule is configured to provide a detectable signal to be read and analyzed.

[0629] FA22. The apparatus according to embodiment FA21, wherein the signal is selected from the group consisting of:

[0630] i. Light emission selected from photoluminescence, electroluminescence, and electrochemiluminescence;

[0631] ii. Light absorption, reflection, transmission, diffraction, scattering, or diffusion;

[0632] iii. Surface Raman scattering;

[0633] iv. Resistive reactance selected from resistors, capacitors, and inductors;

[0634] v. Magnetic relaxation;

[0635] vi. and any combination of iv.

[0636] FA23. The apparatus according to any of the foregoing embodiments, wherein the sample contact area of ​​one or both plates includes binding sites containing a trapping agent, wherein the trapping agent is configured to bind to the target analyte on the cell surface in the sample and immobilize the cells.

[0637] FB2. The method according to embodiment FB1, wherein the deposition step (c) comprises depositing and drying the sample on one or two plates before depositing the remaining portion of the staining solution on top of the dried sample, wherein the sample may be dried in an open configuration thereon, and wherein the sample comprises body fluids selected from: amniotic fluid, aqueous humor, vitreous fluid, blood (e.g., whole blood, graded blood, plasma or serum), breast milk, cerebrospinal fluid (CSF), earwax, chyle, chyme, endolymph, perilymph, feces, respiration, gastric acid, gastric juice, lymph, mucus (including nasal drainage and sputum), pericardial fluid, peritoneal fluid, pleural fluid, pus, rheumatism, saliva, exhaled respiratory condensate, sebum, semen, sputum, sweat, synovial fluid, tears, vomit, urine, and any combination thereof.

[0638] FBB2. The method according to any of the foregoing embodiments, wherein the dyeing solution has a viscosity in the range of 0.1 mPa·s to 3.5 mPa·s.

[0639] FB3. The method according to any of the foregoing embodiments, wherein the deposition step (c) comprises depositing and drying the sample on one or two plates before depositing the remaining portion of the staining solution on top of the dried sample, and wherein the sample comprises a blood smear and is dried on one or two plates.

[0640] FB4. The method according to any of the foregoing embodiments, wherein the deposition step (c) comprises depositing and attaching the sample to one or two plates before depositing the staining solution on top of the sample, wherein the sample contact area of ​​one or two plates adheres to the sample, and wherein the sample is a tissue section with a thickness in the range of 1-200 μm.

[0641] FB5. The apparatus according to embodiment FA4, wherein the sample is paraffin-embedded.

[0642] FB6. The method according to any of the foregoing embodiments, wherein the sample is fixed.

[0643] FB7. The method according to any of the foregoing embodiments, wherein the staining solution contains a fixative capable of fixing the sample.

[0644] FB8. The method according to any of the foregoing embodiments, wherein the staining solution contains a blocking agent, wherein the blocking agent is configured to prevent nonspecific endogenous species in the sample from reacting with the detection agent used to specifically label the target analyte.

[0645] FB9. The method according to any of the foregoing embodiments, wherein the staining solution contains a deparaffinizing agent capable of removing paraffin from the sample.

[0646] B10. The method according to any of the foregoing embodiments, wherein the staining solution contains a permeation agent capable of permeating cells in a tissue sample containing the target analyte.

[0647] FB11. The method according to any of the foregoing embodiments, wherein the staining solution contains an antigen retrieval agent capable of promoting antigen retrieval.

[0648] FB12. The method according to any of the foregoing embodiments, wherein the staining solution contains a detection agent that specifically labels the target analyte in the sample.

[0649] FB13. The method according to any of the foregoing embodiments, wherein the sample contact area of ​​one or both plates includes a storage site containing a blocking agent, wherein the blocking agent is configured to prevent non-specific endogenous species in the sample from reacting with a detection agent used to specifically label a target analyte.

[0650] FB14. The method according to any of the foregoing embodiments, wherein the sample contact area of ​​one or both plates includes a storage site containing a dewaxing agent capable of removing paraffin from the sample.

[0651] FB15. The method according to any of the foregoing embodiments, wherein the sample contact area of ​​one or both plates includes a storage site containing a permeation agent capable of permeating cells in a tissue sample containing the target analyte.

[0652] FB16. The method according to any of the foregoing embodiments, wherein the sample contact area of ​​one or both plates contains a storage site containing an antigen retrieval agent capable of promoting antigen retrieval.

[0653] FB17. The method according to any of the foregoing embodiments, wherein the sample contact area of ​​one or both plates includes a storage site containing a detection agent that specifically labels the target analyte in the sample.

[0654] FB18. The method according to any of the foregoing embodiments, wherein the detection reagent comprises a staining agent selected from the group consisting of: Acid Fuchsin, Alcian Blue 8GX, Alizarin Red S, Aniline Blue WS, Basic Yellow O, Azo Carmine B, Azo Carmine G, Azure A, Azure B, Azure C, Basic Fuchsin, Bismarck Brown Y, Brilliant Cresol Blue, Brilliant Green, Carmine, Chloramphenicol Black E, Congo Red, C1 Cresol Violet, Crystal Violet, Dassard Red, Eosin B, Eosin Y, Erysipelothrix, Ethyl Eosin, Ethyl Green, Fast Green FCF, Fluorescein Isothiocyanate, Giemsa stain, Hematoxylin, Hematoxylin and eosin, indigo carmine, Janus Green B, Janus Green 1899, light green SF, malachite green, Matthew Yellow, methyl orange, methyl violet 2B, methylene blue, methylene blue, methylene violet, (methylene blue), neutral red, aniline black, Nile blue A, nucleoside red, oil red, orange G, orange II, lichen red, pararosaniline, pararosaniline, pararosaniline, pyrrolizin B, pyrrolizin, azurite, rose red, safranin O, Sudan Black B, Sudan III, Sudan V, tetrachromium stain, thionine, toluidine blue, Wiggert, Wright stain, and any combination thereof.

[0655] FB19. The method according to any of the foregoing embodiments, wherein the detection reagent comprises an antibody configured to specifically bind to a protein analyte in the sample.

[0656] FB20. The method according to any of the foregoing embodiments, wherein the detection agent comprises an oligonucleotide probe configured to specifically bind to DNA and / or RNA in a sample.

[0657] FB21. The method according to any of the foregoing embodiments, wherein the detection agent is labeled with a reporter molecule, wherein the reporter molecule is configured to provide a detectable signal to be read and analyzed.

[0658] FB22. In some embodiments, FB21, the signal is selected from a group consisting of the following:

[0659] i. Light emission selected from photoluminescence, electroluminescence, and electrochemiluminescence;

[0660] ii. Light absorption, reflection, transmission, diffraction, scattering, or diffusion;

[0661] iii. Surface Raman scattering;

[0662] iv. Resistive reactance selected from resistors, capacitors, and inductors;

[0663] v. Magnetic relaxation;

[0664] vi. and any combination of iv.

[0665] FB23. The method according to any of the foregoing embodiments, wherein the sample contact area of ​​one or both plates contains a binding site containing a trapping agent, wherein the trapping agent is configured to bind to the target analyte on the cell surface in the sample and immobilize the cells.

[0666] FB24. The method according to any of the foregoing embodiments, prior to step (e), further comprises: incubating the sample in a closed configuration for a period of time longer than the time it takes for the detector to diffuse through the uniform thickness layer and the sample.

[0667] FB25. The method according to any of the foregoing embodiments, prior to step (e), further comprises: incubating the sample in a closed configuration at a predetermined temperature in the range of 30-75°C.

[0668] FB26. The method according to any of the foregoing embodiments, wherein the staining solution comprises a transfer solution.

[0669] G. Dual-lens imaging system

[0670] However, dual cameras are becoming increasingly common in existing smartphones, offering more possibilities for smartphone-based imaging. By using two cameras, two different regions of a sample can be imaged simultaneously, which equates to a much larger field of view. Furthermore, each camera can be used for microscopic imaging at different resolutions. For example, one camera can perform microscopy with a lower resolution but a larger field of view to image large objects in the sample, while the other camera can perform microscopy with a higher resolution but a smaller field of view to image small objects. This is useful when the sample used for imaging contains a mixture of small and large objects. Therefore, providing users with smartphone imaging systems based on dual cameras is highly anticipated.

[0671] Dual-camera imaging system

[0672] Figure 19A This is a schematic diagram of a dual-camera imaging system. The dual-camera imaging system includes a mobile computing device (e.g., a smartphone) with two built-in camera modules, two external lenses, a QMAX device, and a light source. Each camera module has an internal lens and an image sensor. The QMAX device is located below the two camera modules. Each external lens is positioned at an appropriate height between the QMAX device and its corresponding internal lens, allowing the sample in the QMAX device to be clearly focused onto the image sensor. Each external lens is aligned with its corresponding internal lens. Light captured by the imaging sensor can be refracted from the sample, emitted from the sample, etc. The light captured by the imaging sensor covers the visible wavelength and can illuminate the sample in the QMAX device from the rear or top side at a vertical or oblique angle of incidence.

[0673] Dual-camera imaging system for large field-of-view imaging

[0674] One implementation is a dual-camera imaging system for large field-of-view (FOV) imaging. In this implementation, the images captured by both cameras have the same scale or optical magnification. For this purpose, an external lens 1f... E1 focal length, internal lens 1f N1 focal length, external lens 2f E2 focal length and internal lens 2f N2 The focal lengths satisfy the following relationship:

[0675] Choose an appropriate distance between the two cameras so that their field of view (FOV) overlaps. For example... Figure 19B As shown, the letter "A" represents the sample. Due to the overlap between the FOVs of the two cameras, part of the letter "A" exists in both the FOV of camera 1 and the FOV of camera 2.

[0676] Another image processing step is used to merge the two images into a large image by matching the same features shared by the two images taken by camera 1 and camera 2.

[0677] Dual-camera imaging system for dual-resolution imaging

[0678] Lens-based imaging systems inherently involve a trade-off between FOV size and resolution. Achieving a large FOV requires sacrificing the imaging system's resolution. This issue becomes more pronounced when the sample contains a mixture of small and large objects with significantly different size scales. To image a sufficient number of large objects, the FOV needs to be large enough, but this results in a loss of resolution to capture details of the smaller objects. To address this problem, in this embodiment, a dual-camera imaging system is used to achieve dual-resolution imaging on the same sample, where camera 1 (or 2) is used for low-resolution and large FOV imaging, and camera 2 (or 1) is used for high-resolution and small FOV imaging.

[0679] The resolution of an imaging system depends on its optical magnification, which is equal to the ratio of the focal length of the external lens to the focal length of the internal lens. For example, in this embodiment, camera 1 is used for low-resolution imaging, and camera 2 is used for high-resolution imaging; therefore, the external lens 1f... E1 focal length, internal lens 1f N1 Focal length, external lens 2 fE 2 focal length and internal lens 2f N2 The focal lengths satisfy the following relationship:

[0680] The field of view (FOV) of the two cameras may or may not overlap.

[0681] like Figure 19CAs shown, the sample image captured by camera 1 covers a larger FOV and contains more objects within a single FOV, but cannot resolve details of small objects. The image captured by camera 2 covers a relatively smaller FOV and contains fewer objects within a single FOV, but has a higher resolution capable of resolving details within small objects.

[0682] Embodiments of the present invention

[0683] A1. A dual-lens imaging device, comprising:

[0684] The components include a first external lens, a second external lens, a housing unit, and a card unit, wherein:

[0685] i. The housing unit is configured to accommodate the first external lens, the second external lens, and the card unit, and connects the dual-length imaging device to the moving device;

[0686] ii. The first and second external lenses are configured to be aligned with the two internal lenses in the moving device, respectively; and

[0687] iii. The card unit is configured to accommodate a sample card containing a sample.

[0688] The card unit is located between the outer lens and the inner lens;

[0689] The external lens is configured to focus illumination light refracted or emitted from the sample card onto the image sensor in the moving device, thereby allowing the image sensor to capture an image of the sample.

[0690] B1. A dual-lens imaging system, comprising:

[0691] (a) The dual-lens imaging device of A1 as described in the implementation scheme.

[0692] (b) The mobile device includes hardware and software for capturing and processing sample images via a dual-lens imaging device.

[0693] C1. The apparatus or system according to any of the foregoing embodiments, wherein the sample card is a QMAX card.

[0694] C2. The apparatus or system according to any of the foregoing embodiments, wherein the mobile device is a mobile communication device.

[0695] C3. The apparatus or system according to any of the foregoing embodiments, wherein the mobile device is a smartphone.

[0696] C4. The apparatus or system according to any of the foregoing embodiments, wherein the moving device includes a light source that provides light to the sample card.

[0697] C5. The apparatus or system according to any of the foregoing embodiments, wherein the two external lenses are configured to capture overlapping images that are at least partially overlapping.

[0698] C6. The apparatus or system according to embodiment C5, wherein the overlapping images have the same resolution.

[0699] C7. The apparatus or system according to embodiment C6, wherein the software is configured to process overlapping images to generate a combined image of the sample.

[0700] C8. The apparatus or system according to embodiment C5, wherein the overlapping images have different resolutions.

[0701] C9. The apparatus or system according to embodiment C8, wherein the software is configured to process overlapping images illustrating specific portions of the image with lower resolution.

[0702] C10. The apparatus or system according to any of the foregoing embodiments, wherein the two external lenses are configured to image two different locations of the sample region of the Q card.

[0703] C11. The apparatus or system according to any of the foregoing embodiments, wherein the two external lenses are configured to have different sizes of field of view.

[0704] C12. The apparatus or system according to any of the foregoing embodiments, wherein the two external lenses are configured to have different FoVs (fields of view) and wherein the ratio of the two different FoVs is 1.1, 1.2, 1.5, 2, 5, 10, 15, 20, 30, 50, 100, 200, 1000 or any value of both. Preferred ratios are 1.2, 1.5, 2, 5, 10, 20 or any value of both.

[0705] C13. The apparatus or system according to any of the foregoing embodiments, wherein the overlap of the FoV of the two external lenses is configured to be within a range of about 1%, 5%, 10%, 20%, 50%, 60%, 70%, 80%, 90%, or any of these values.

[0706] C14. The apparatus or system according to any of the foregoing embodiments, wherein the two external lenses are optically coupled to different filters and / or polarizers.

[0707] Other implementation plans

[0708] An optical adapter for imaging a sample using a handheld imaging device having a light source, a single camera, and a computer processor, the optical adapter comprising:

[0709] shell;

[0710] The cavity inside the outer shell; and

[0711] The lever inside the cavity,

[0712] The lever includes at least one optical element and is configured to move between a first position and a second position, wherein (i) in the first position, the imaging device is capable of imaging the sample in bright field mode, and (ii) in the second position, the imaging device is capable of imaging the sample in fluorescence excitation mode.

[0713] An optical adapter for imaging a sample using a handheld imaging device having a light source, a single camera, and a computer processor, the optical adapter comprising:

[0714] shell;

[0715] The lens is arranged to provide a field of view to the camera;

[0716] A cavity within the housing for receiving and positioning the sample within the camera's field of view, wherein a lens is positioned to receive light refracted or emitted by the sample when within the camera's field of view; and

[0717] The lever inside the cavity,

[0718] The lever includes at least one optical element and is configured to move between a first position and a second position, wherein (i) in the first position, the imaging device is capable of imaging the sample in bright field mode, and (ii) in the second position, the imaging device is capable of imaging the sample in fluorescence excitation mode.

[0719] An optical adapter for imaging a sample using a handheld imaging device having a light source, a single camera, and a computer processor, the optical adapter comprising:

[0720] shell;

[0721] The cavity inside the housing is used to receive the sample and position it within the camera's field of view; and

[0722] The lever inside the cavity,

[0723] The lever includes at least one optical element and is configured to move between a first position and a second position, wherein (i) in the first position, the imaging device is capable of imaging the sample in bright-field mode, and (ii) in the second position, the imaging device is capable of imaging the sample in fluorescence-excited mode.

[0724] The lever includes a first planar region extending along a first plane and a second planar region laterally shifted from the first planar region along a first direction and extending along a second plane. The first plane is arranged at a different height from the second plane along the second direction, which is perpendicular to the first direction.

[0725] An optical adapter for imaging a sample using a handheld imaging device having a light source, a single camera, and a computer processor, the optical adapter comprising:

[0726] shell;

[0727] The cavity inside the housing is used to receive the sample and position it within the camera's field of view; and

[0728] The lever inside the cavity,

[0729] The lever includes at least one optical element and is configured to move between a first position and a second position, wherein (i) in the first position, the imaging device is capable of imaging the sample in bright-field mode, and (ii) in the second position, the imaging device is capable of imaging the sample in fluorescence-excited mode.

[0730] The lever includes a first planar region extending along a first plane and a second planar region laterally shifted from the first planar region along a first direction and extending along a second plane. The first plane is positioned at a different height from the second plane along the second direction, which is perpendicular to the first direction.

[0731] The first planar region contains at least one optical element, and the second planar region contains at least one optical element.

[0732] An optical adapter for imaging a sample using a handheld imaging device having a light source, a single camera, and a computer processor, the optical adapter comprising:

[0733] shell;

[0734] The cavity inside the outer shell; and

[0735] The lever inside the cavity,

[0736] The lever includes at least one optical element and is configured to move between at least three different positions, wherein (i) in a first position, the imaging device is capable of imaging the sample in bright field mode, (ii) in a second position, the imaging device is capable of imaging the sample in fluorescence excitation mode, and (iii) in a third position, the imaging device is capable of measuring the light absorption of the sample.

[0737] An optical adapter for imaging a sample using a handheld imaging device having a light source, a single camera, and a computer processor, the optical adapter comprising:

[0738] shell;

[0739] Lenses are constructed to provide the camera's field of view;

[0740] The cavity inside the housing is used to receive the sample and position it within the camera's field of view;

[0741] An aperture within the housing, wherein the aperture is arranged to receive source light from a light source for illuminating the sample; and

[0742] The lever inside the cavity

[0743] The lever includes at least one optical element and is configured to move between a first position and a second position, wherein (i) in the first position, the imaging device is capable of imaging the sample in a bright field mode, and (ii) in the second position, the imaging device is capable of imaging the sample in a fluorescence excitation mode, wherein in the fluorescence excitation mode, a lens is arranged to receive light emitted by the sample when the sample is illuminated by a light source.

[0744] An optical adapter for imaging a sample using a handheld imaging device having a light source, a single camera, and a computer processor, the optical adapter comprising:

[0745] shell;

[0746] Lenses are constructed to provide the camera's field of view;

[0747] The cavity inside the housing is used to receive the sample and position it within the camera's field of view;

[0748] The lever inside the cavity

[0749] The lever includes at least one optical element and is configured to move between a first position and a second position, wherein (i) in the first position, the imaging device is capable of imaging the sample in bright field mode, and (ii) in the second position, the imaging device is capable of imaging the sample in fluorescence excitation mode.

[0750] An optical component is attachable to a handheld electronic device having a light source, a camera, and a computer processor, wherein the optical component is configured to enable microscopic imaging of a sample by the camera when the sample is illuminated by light from the light source, the optical component comprising:

[0751] shell;

[0752] The cavity inside the outer shell;

[0753] Lenses configured to provide a microscopic field of view to a camera; and

[0754] An active arm within a cavity, wherein the active arm is configured to switch between a first position and a second position, wherein when the active arm is in the first position, the optical component is in bright-field mode, and when the active arm is in the second position, the optical component is in fluorescence excitation mode.

[0755] The optical component according to any embodiment, wherein the housing comprises:

[0756] The sample receiving area within the cavity; and

[0757] A slot on one side of the housing, wherein the slot is arranged to receive the sample substrate in the sample receiving area and position the sample within the field of view of the camera.

[0758] The optical assembly described in the embodiment further includes one or more optical elements in a first group, the one or more optical elements in the first group being arranged to receive light entering from a first aperture in the housing corresponding to a light source and to redirect the light entering from the first aperture along a first path to a second aperture in the housing corresponding to a camera to provide bright-field illumination of the sample when the movable arm is in a first position.

[0759] The optical assembly described in the embodiment includes a first group of one or more optical elements comprising a first right-angle mirror and a second right-angle mirror, wherein the first and second right-angle mirrors are in a first path and arranged to reflect light from a light source so as to be incident perpendicularly into the camera.

[0760] The optical component described in the implementation scheme, wherein the light source is a point source, is used to achieve interferometric imaging of a transparent sample by illuminating the sample with the same wavefront.

[0761] The optical assembly described in the embodiment further includes a second group of one or more optical elements, which are mechanically coupled to the movable arm and arranged to receive light entering from the first aperture and to change the direction of the light entering from the first aperture along a second path to obliquely illuminate the sample so as to provide fluorescence illumination of the sample when the movable arm is in the second position.

[0762] The optical component described in the embodiment has an oblique angle greater than the collection angle of the lens, and the lens is configured to provide the field of view of the camera.

[0763] The optical assembly described in the embodiment, wherein one or more optical elements of the second group include a mirror and an optical absorber, wherein the mirror reflects light to obliquely illuminate the sample and the optical absorber absorbs external light from the first aperture, which would otherwise pass through the second aperture of the housing and cover the camera in fluorescence excitation mode.

[0764] The optical component described in the embodiment, wherein the absorber absorbs light that has not been incident on the mirror after passing through the first aperture, wherein the light absorber is a thin-film light absorber.

[0765] The optical assembly described in the embodiment further includes one or more optical elements in a third group, which are arranged to receive light entering from the first aperture and redirect light entering from the second aperture in the movable arm and travel along a first path toward a light diffuser on the movable arm to illuminate the sample in a normal direction for measuring the light absorption of the sample.

[0766] The optical assembly described in the embodiment, wherein one or more optical elements of the third group include a light diffuser, a first right-angle mirror and a second right-angle mirror, wherein the first right-angle mirror and the second right-angle mirror are located in a first path and are arranged to reflect light from the light source to the light diffuser and then incident perpendicularly into the camera;

[0767] The optical component described in the implementation scheme, wherein the light diffuser is a semi-transparent diffuser with an opacity ranging from 10% to 90%.

[0768] The optical component described in the embodiment further includes a rubber door to cover the sample receiver to prevent ambient light from entering the cavity.

[0769] The optical components described in any of the foregoing embodiments, wherein the light source and the camera are positioned on the same side of the handheld electronic device at a fixed distance from each other.

[0770] A system comprising: an optical component as described in any of the preceding embodiments, and a mobile phone accessory, the mobile phone accessory including a first side configured to be coupled to the optical component and a second opposite side configured to be coupled to a handheld electronic device, wherein the handheld electronic device is a mobile phone.

[0771] The system described in any embodiment, wherein the mobile phone accessory is replaceable to provide accessories for mobile phones of different sizes.

[0772] The system described in any embodiment, wherein the size of the mobile phone accessory is adjustable.

[0773] An optical component for a handheld mobile electronic device, the optical component comprising:

[0774] shell;

[0775] The cavity inside the outer casing;

[0776] Multiple optical elements are arranged within the cavity to receive light entering from a first aperture in the housing and to redirect the light entering from the first aperture along a first path toward a second aperture in the housing.

[0777] A movable arm that can be constructed in at least two different locations within the housing, or a movable arm that can be constructed in at least three different locations within the housing.

[0778] The movable arm includes a light reflector section for reflecting light.

[0779] The movable arm includes a light diffuser to homogenize the light and destroy its coherence.

[0780] The movable arm includes an aperture that is aligned with the inlet aperture in the housing.

[0781] When the movable arm is in its first position within the housing, the light reflector is positioned between the inlet aperture and multiple optical elements within the housing, thus blocking light entering from the first opening from incident on the multiple optical elements.

[0782] When the movable arm is in the second position inside the housing, light entering from the first opening is incident on multiple optical elements, and when the movable arm is in the third position inside the housing, light entering from the first opening passes through the aperture on the movable arm and then incident on the light diffuser.

[0783] The optical component of any embodiment includes a slot on one side of the housing, wherein the slot is arranged to receive a sample substrate such that:

[0784] When the sample substrate is fully inserted into the slot and the movable arm is in the second position inside the housing, the first path intersects with the sample substrate; and

[0785] When the sample substrate is fully inserted into the slot and the movable arm is in the first position inside the housing, the light partially reflected by the light reflector is redirected to the sample substrate; and

[0786] When the sample substrate is fully inserted into the slot and the movable arm is in the third position inside the housing, the light travels along the first path toward the light diffuser and then illuminates the sample substrate.

[0787] The optical assembly of any embodiment, wherein the movable arm includes a light-absorbing portion to absorb light that has not been incident on the mirror after passing through the first aperture.

[0788] The optical component according to any embodiment, wherein the movable arm comprises:

[0789] The first receiver is positioned above the light reflector section; and

[0790] An optical filter is disposed in the receiver; a second housing is located above the aperture portion; and a filter is located in the receiver.

[0791] The optical component according to any embodiment, wherein when the movable arm is in a first position, a filter disposed in the receiver is positioned to receive light entering from a first aperture in the housing; and when the movable arm is in a third position, a filter located in the receiver is positioned to receive light entering from the first aperture in the housing.

[0792] In any embodiment of the optical component, when the movable arm is in the first position and the sample substrate is fully inserted into the slot, the filter located in the receiver overlaps with a portion of the sample substrate.

[0793] A system comprising:

[0794] The optical components described in any embodiment; and

[0795] A mobile phone accessory, comprising a first side configured to be attached to an optical component and a second opposite side configured to be attached to a mobile phone, wherein the size of the mobile phone accessory is adjustable.

[0796] An optical component is attachable to a handheld electronic device having a light source, a camera, and a computer processor, wherein the optical component is configured to enable microscopic imaging of a sample by a camera when the sample is illuminated by light from the light source. The optical component comprises:

[0797] A lens configured to provide a microscopic field of view to the camera;

[0798] A receiver used to receive and position samples within the microscopic field of view;

[0799] Optical fiber is constructed to receive light from a light source and illuminate a receiver.

[0800] The optical component described in any embodiment, wherein when the optical component is attached to a handheld electronic device, the lens and camera define the optical axis, and wherein the optical fiber surrounds the optical axis.

[0801] The optical component described in any embodiment, wherein the optical fiber is ring-shaped.

[0802] The optical component described in any embodiment, wherein the optical fiber is a side-emitting optical fiber.

[0803] The optical component of any embodiment includes a housing defining a receiver, wherein a ring fiber is located in a recess in the housing, and wherein the housing includes an aperture configured to align with two end faces of the light source and the ring fiber to receive light from the light source.

[0804] The optical component described in any embodiment, wherein light is emitted from the side of the ring fiber to illuminate a sample region directly below the camera along the optical axis.

[0805] The optical component of any embodiment includes a housing defining a receiver, wherein the housing includes a first aperture configured to align with a light source, and a first end face of an optical fiber is positioned within the first aperture to receive light from the light source.

[0806] The optical component of any embodiment includes a housing comprising a second aperture configured to be aligned with a camera, and an optical fiber comprising a first end positioned in a first aperture and a second end positioned in a second aperture.

[0807] In any embodiment of the optical component, at least one of the first end face and the second end face of the optical fiber is entangled.

[0808] The optical component described in any embodiment, wherein when the optical component is attached to a handheld electronic device, the optical fiber is tilted relative to the light source, and

[0809] The second end face of the optical fiber is arranged to illuminate the area of ​​the sample located directly below the lens.

[0810] The optical component of any embodiment includes a housing defining a receiver, the housing including a recess in which an optical fiber is disposed.

[0811] An optical component is attachable to a handheld electronic device having a light source, a camera, and a computer processor, wherein the optical component is configured to enable microscopic imaging of a sample by a camera when the sample is illuminated by light from the light source. The optical component comprises:

[0812] A lens configured to provide a microscopic field of view to the camera;

[0813] A receiver used to receive and position samples within the microscopic field of view;

[0814] A reflecting mirror, offset from the optical axis of the lens and positioned to reflect light from the light source and illuminate the sample within a range of tilt angles relative to the optical axis; and

[0815] A wavelength filter is positioned between the sample and the camera to allow fluorescence emitted by the sample to pass through in response to oblique illumination.

[0816] The optical assembly of any embodiment, wherein a lens is positioned on the front side of the sample and a reflector is positioned to illuminate the sample at an angle from the rear side of the sample, wherein the angle of tilt is greater than the collection angle of the lens.

[0817] The optical component described in any embodiment further includes an optical absorber positioned on the optical axis adjacent to the reflector to absorb light from the light source that has not been reflected by the reflector.

[0818] The optical assembly described in any embodiment, wherein the reflector and the optical absorber are mounted on a common structure and tilted relative to each other.

[0819] The optical component described in any embodiment further includes a second wavelength filter positioned in the path of the illumination light between the light source and the mirror to select certain wavelengths for illuminating the sample.

[0820] The optical component described in any of the foregoing embodiments, wherein the sample is supported by a sample holder comprising a planar structure, and wherein the receiver is configured to position the planar structure to partially extend into the path of the illumination light from the light source to connect the illumination light to the planar structure.

[0821] The optical assembly of Embodiment 6, wherein the receiver is configured to position the planar structure such that the illumination light path is incident on the edge of the planar structure, wherein the edge extends along a plane perpendicular to the plane containing the field of view.

[0822] The optical component of any embodiment, wherein the mirror is arranged to reflect light to partially obliquely illuminate the sample from the rear side of the planar structure and partially illuminate the edge of the planar structure to connect the illumination light into the planar structure.

[0823] The optical component described in any embodiment further includes a rubber door to cover the sample receiver to prevent ambient light from entering the optical component and the camera.

[0824] The optical component described in any embodiment, wherein the planar structure is configured to guide the coupled illumination light waveguide to the sample to illuminate the sample and cause the sample to emit fluorescence.

[0825] The optical component described in any embodiment further includes a sample holder.

[0826] The optical component of any embodiment, wherein the sample is a liquid sample and the sample holder includes a first plate and a second plate for holding the liquid sample.

[0827] The optical assembly described in any of the foregoing embodiments, wherein the lens, receiver, mirror, and wavelength filter are supported in a common optical box, and the optical assembly further includes a replaceable retainer frame for attaching the optical box to a handheld electronic device.

[0828] The optical components described in any embodiment, wherein the light source and the camera are positioned on the same side of the handheld electronic device and are a fixed distance apart from each other.

[0829] The optical component described in any embodiment, wherein the handheld electronic device is a mobile phone.

[0830] An apparatus comprising the optical components and handheld electronic device described in any of the foregoing embodiments.

[0831] An optical component, attachable to a handheld electronic device having a light source, a camera, and a computer processor, wherein the optical component is configured to enable microscopic imaging of a sample by the camera when the sample is illuminated by light from the light source, the optical component comprising:

[0832] Lenses configured to provide a microscopic field of view to a camera;

[0833] The receiver is used to receive the sample and position it within the microscope's field of view.

[0834] The sample is supported by a sample holder comprising a planar structure, and a receiver is configured to position the planar structure to partially extend into the path of illumination light from the light source, thereby coordinating the illumination light into the planar structure and causing the sample to emit fluorescence; and

[0835] A wavelength filter is positioned between the sample and the camera to allow fluorescence emitted by the sample in response to illumination to pass through.

[0836] The optical component described in any embodiment further includes a rubber door covering the sample receiver to prevent ambient light from entering the optical component through the receiver.

[0837] The optical component described in any embodiment, wherein the planar structure is configured to guide a coupled illumination light waveguide to the sample to illuminate the sample and cause the sample to emit fluorescence.

[0838] The optical component described in any embodiment further includes a sample holder.

[0839] The optical component of any embodiment, wherein the sample is a liquid sample and the sample holder includes a first plate and a second plate for holding the liquid sample.

[0840] The optical component of any embodiment further includes a second wavelength filter located in the path of the illumination light between the light source and a portion of the sample holder that extends into the optical path.

[0841] The optical assembly described in any of the foregoing embodiments, wherein the lens, receiver, and wavelength filter are supported in a common optical box, and the optical assembly further includes a replaceable retainer frame for attaching the optical box to a handheld electronic device.

[0842] The optical components described in any embodiment, wherein the light source and the camera are positioned at a fixed distance from each other on the same side of the handheld electronic device.

[0843] The optical component described in any embodiment, wherein the handheld electronic device is a mobile phone.

[0844] An apparatus comprising the optical components and handheld electronic device described in any of the foregoing embodiments.

[0845] An optical component is attachable to a handheld electronic device having a light source, a camera, and a computer processor, wherein the optical component is configured to enable microscopic imaging of a sample by a camera when the sample is illuminated by light from the light source. The optical component comprises:

[0846] A first mounting lens is configured to provide a first microscopic field of view to a first camera module;

[0847] A second mounting lens, configured to provide a second microscopic field of view to the second camera module; and

[0848] The receiver is used to receive the sample and position the sample within the first and second microscopic fields of view.

[0849] The optical component according to any embodiment, wherein the first camera module includes a first internal lens and the second camera module includes a second internal lens, wherein the first optical magnification provided by the first mounting lens and the first internal lens is the same as the second optical magnification provided by the second mounting lens and the second internal lens.

[0850] In any embodiment of the optical component, a first ratio of the focal length of the first mounting lens to the focal length of the first internal lens is equal to a second ratio of the focal length of the second mounting lens to the focal length of the second internal lens.

[0851] The optical component described in any embodiment, wherein the first image resolution provided by the first camera module and the first mounting lens is the same as the second image resolution provided by the second camera module and the second mounting lens.

[0852] The optical component described in any embodiment, wherein the first camera module includes a first internal lens and the second camera module includes a second internal lens, wherein the first optical magnification provided by the first mounting lens and the first internal lens is different from the second optical magnification provided by the second mounting lens and the second internal lens.

[0853] In any embodiment of the optical component, a first ratio of the focal length of the first mounting lens to the focal length of the first internal lens is less than a second ratio of the focal length of the second mounting lens to the focal length of the second internal lens.

[0854] The optical component of any embodiment, wherein the first image resolution provided by the first camera module and the first mounting lens is less than the second image resolution provided by the second camera module and the second mounting lens.

[0855] The optical component described in any of the foregoing embodiments, wherein the first microscopic field of view overlaps with the second microscopic field of view.

[0856] The optical component described in any embodiment, wherein the overlap between the first and second microscopic fields of view is between 1% and 90%.

[0857] The optical component described in any embodiment, wherein the first microscopic field of view does not overlap with the second microscopic field of view.

[0858] The optical component described in any of the foregoing embodiments, wherein each of the first and second assembly lenses is arranged to receive light scattered or emitted by the sample.

[0859] The optical component described in any of the foregoing embodiments, wherein the first microscopic field of view is smaller than the second microscopic field of view.

[0860] In any of the aforementioned embodiments, the angular field of view of the first assembled lens is smaller than that of the second assembled lens.

[0861] The optical component according to any embodiment, wherein the ratio of the angular field of view of the first mounted lens to the angular field of view of the second mounted lens is between 1.1 and 1000.

[0862] The optical component described in any embodiment includes:

[0863] A first filter, the first filter being arranged in a first illumination path leading to or from a first mounting lens; and

[0864] The second filter is arranged in the second illumination path leading to or from the second assembled lens.

[0865] The optical component described in any embodiment, wherein a first filter is configured to filter a first wavelength range, a second filter is configured to filter a second wavelength range, and the first wavelength range is different from the second wavelength range.

[0866] The optical component described in any embodiment includes:

[0867] A first polarizer is arranged in a first illumination path leading to or from a first assembled lens; and

[0868] A second polarizer is arranged in the second illumination path leading to or from the second assembled lens.

[0869] The optical component described in any embodiment, wherein the first polarizer and the second polarizer have different polarization-dependent light transmission and blocking characteristics.

[0870] An apparatus comprising the optical components and handheld electronic device described in any of the foregoing embodiments.

[0871] The optical component described in any embodiment, wherein the handheld electronic device is a mobile phone.

[0872] The apparatus according to any embodiment, wherein the handheld electronic device is configured to computationally merge a first image obtained from a first camera module with a second image obtained from a second camera module.

[0873] An imaging method, comprising:

[0874] A sample is compressed between two plates, which are separated from each other by an array of spacers, at least one of which has a reference mark.

[0875] Multiple images of the sample are acquired using an imaging system comprising a camera and at least one lens, wherein each image corresponds to a different surface within the sample thickness;

[0876] Based on one or more reference markers, each image is calculated and analyzed to determine information about the corresponding object plane; and

[0877] A three-dimensional image of the sample is computationally constructed based on multiple images and information about the corresponding object plane.

[0878] The imaging method described in any of the foregoing embodiments, wherein the determined information about the corresponding object surface includes the depth of the object surface relative to the imaging system.

[0879] The imaging method according to any embodiment 2, wherein at least some spacers each have a reference mark.

[0880] In any of the foregoing embodiments of the imaging method, the determined information about the corresponding object plane includes the depth and orientation of the object plane relative to the imaging system.

[0881] The imaging method described in any of the foregoing embodiments, wherein computational analysis of each image includes determining the degree of defocus of one or more reference markers.

[0882] The imaging method described in any of the foregoing embodiments, wherein the computational analysis of each image includes: determining the depth of each of the plurality of reference markers based on the defocus of each reference marker; and determining the depth and orientation of the corresponding object plane relative to the imaging system based on the determined depth of the reference markers.

[0883] The imaging method described in any of the foregoing embodiments, wherein the reference marker is not rotationally symmetric with respect to an axis perpendicular to at least one of the plates.

[0884] The imaging method described in any of the foregoing embodiments, wherein computational analysis of each image includes determining the rotational orientation of one or more reference markers relative to the axis of the imaging system.

[0885] The imaging method described in any of the foregoing embodiments, wherein computational analysis of each image includes comparing image information about a reference marker with prior knowledge about the reference marker.

[0886] The imaging method described in any of the foregoing embodiments, wherein prior knowledge about the reference markers is based on one or more of the shape of each reference marker and the position of each reference marker relative to the plate.

[0887] In any of the aforementioned embodiments of the imaging method, the spacer is a columnar body.

[0888] The imaging method described in any of the foregoing embodiments, wherein acquiring multiple images includes one or more components of an imaging system that moves relative to a plate holding the sample.

[0889] The imaging method described in any of the foregoing embodiments, wherein the computational construction of the three-dimensional image includes processing each acquired image to remove defocus features.

[0890] The imaging method described in any of the foregoing embodiments, wherein processing each acquired image to remove defocus features includes using a bandpass filter.

[0891] The imaging method described in any of the foregoing embodiments, wherein the acquired image corresponds to an interference image formed by combining light from the sample with reference light from the sample not directed to the camera.

[0892] An imaging device comprising:

[0893] An imaging system comprising a camera and at least one lens;

[0894] A sample holder for supporting a sample cassette relative to an imaging system, the sample cassette comprising two plates separated from each other by an array of spacers, at least one having a reference mark, wherein the sample to be imaged is configured to be compressed between the two plates; and

[0895] A processing and control system is coupled to the sample holder and camera and configured to acquire multiple images of the sample using an imaging system, each image corresponding to a different object plane within the sample's thickness.

[0896] The processing and control system is further configured as follows:

[0897] Each image is calculated and analyzed based on one or more reference markers to determine information about the corresponding object plane; and

[0898] A three-dimensional image of the sample is computationally constructed based on multiple images and information about the corresponding object plane.

[0899] The imaging apparatus described in any of the foregoing embodiments, wherein the determined information about the corresponding object surface includes the depth of the object surface relative to the imaging system.

[0900] The imaging apparatus of any embodiment, or at least some of the spacers therein, each has a reference mark.

[0901] The imaging apparatus described in any of the foregoing embodiments, wherein the determined information about the corresponding object plane includes the depth and orientation of the object plane relative to the imaging system.

[0902] The apparatus described in any of the foregoing embodiments, wherein the computational analysis of each image includes determining the degree of defocus of one or more of the reference markers.

[0903] The apparatus of embodiment 20, wherein computational analysis of each image includes: determining the depth of each of a plurality of reference markers based on the defocus of each reference marker; and determining the depth and orientation of the corresponding object plane relative to the imaging system based on the determined depth of the reference markers.

[0904] The apparatus of any of the foregoing embodiments, wherein the reference mark is not rotationally symmetrical with respect to an axis perpendicular to at least one of the plates.

[0905] The apparatus of any embodiment wherein computational analysis of each image includes determining the rotational orientation of one or more reference markers relative to the axis of the imaging system.

[0906] The apparatus described in any of the foregoing embodiments, wherein computational analysis of each image includes comparing image information about the reference marker with prior knowledge about the reference marker.

[0907] The apparatus described in any of the foregoing embodiments, wherein prior knowledge about the reference marks is based on one or more of the shape of each reference mark and the position of each reference mark relative to the plate.

[0908] In any of the foregoing embodiments of the device, the spacer is a cylindrical body.

[0909] The apparatus described in any of the foregoing embodiments, wherein the control system is configured to move one or more components of the imaging system relative to the plate holding the sample to acquire multiple images.

[0910] The apparatus described in any of the foregoing embodiments, wherein the computational construction of the three-dimensional image includes processing each acquired image to remove defocus features.

[0911] The apparatus of any embodiment wherein processing each acquired image to remove defocus features includes using a bandpass filter.

[0912] The apparatus described in any of the foregoing embodiments, wherein the acquired image corresponds to an interference image formed by combining light from the sample with reference light from the sample not directed to the camera.

[0913] More other implementation schemes

[0914] This invention includes various embodiments that can be combined in multiple ways as long as the various components do not contradict each other. The embodiments should be considered as a single inventive document: each application has other applications referenced as references, and is also cited in its entirety for all purposes, rather than as discrete, independent documents. These embodiments include not only the disclosure in this document, but also the documents cited, incorporated, or claiming priority herein.

[0915] (1) definition

[0916] The terms used to describe the apparatus, systems, and methods disclosed herein are defined in this application or in PCT applications (designated U.S.) filed August 10, 2016 and September 14, 2016, respectively, U.S. Provisional Application No. 62 / 456065 filed February 7, 2017, U.S. Provisional Application No. 62 / 426065 filed February 8, 2017, and U.S. Provisional Application No. 62 / 456504 filed February 8, 2017, the entire contents of all such applications are incorporated herein for all purposes.

[0917] The terms “CROF card (or card)”, “COF card”, “QMAX card”, “Q card”, “CROF device”, “COF device”, “QMAX device”, “CROF plate”, “COF plate”, and “QMAX-plate” are interchangeable, except in some embodiments where the COF card does not include a spacer; and these terms refer to a device comprising a first plate and a second plate, the first plate and the second plate being movable relative to each other into different configurations (including open configurations and closed configurations), and the device comprising a spacer for adjusting the spacing between the plates (except in some embodiments of COF). The term “X-plate” refers to one of the two plates in a CROF card to which the spacer is fixed. Further description of the COF card, CROF card, and X-plate is described in Provisional Application Serial No. 62 / 456065, filed February 7, 2017, all of which are incorporated herein by reference in their entirety for all purposes.

[0918] (2) Q-card, spacer, and uniform sample thickness

[0919] The apparatus, systems, and methods disclosed herein may include or utilize Q-cards, spacers, and embodiments for uniform sample thickness for sample detection, analysis, and quantification. In some embodiments, the Q-card includes spacers that facilitate making at least a portion of the sample a highly homogeneous layer. The structure, materials, functions, variations, and dimensions of spacers, as well as the homogeneity of spacers and sample layers, are disclosed, described, and summarized herein in or listed in, or in, U.S. Provisional Application Nos. 62 / 456065, filed August 10, 2016 and September 14, 2016, respectively; U.S. Provisional Application Nos. 62 / 426065, filed February 7, 2017; U.S. Provisional Application No. 62 / 456504, filed February 8, 2017; and all the contents of all these applications are incorporated herein for all purposes.

[0920] (3) Hinges, open notches, recessed edges and sliders

[0921] The apparatuses, systems, and methods disclosed herein may include or use Q-cards for sample detection, analysis, and quantification. In some embodiments, the Q-card includes hinges, notches, recesses, and sliders that facilitate the operation of the Q-card and the measurement of the sample. The structure, materials, functions, variations, and dimensions of hinges, notches, recesses, and sliders are disclosed, described, and summarized herein in or listed in, or in, U.S. Provisional Application No. 62 / 456065, filed August 10, 2016 and September 14, 2016, respectively; U.S. Provisional Application No. 62 / 426065, filed February 7, 2017; U.S. Provisional Application No. 62 / 456504, filed February 8, 2017; and U.S. Provisional Application No. 62 / 456504, filed February 8, 2017, respectively, all of which are incorporated herein by reference in their entirety for all purposes.

[0922] (4) Q-card, slider, and smartphone detection system

[0923] The apparatus, systems, and methods disclosed herein may include or use Q-cards for sample detection, analysis, and quantification. In some embodiments, the Q-card is used in conjunction with a slider that allows a smartphone detection system to read the card. The structure, materials, functions, variations, dimensions, and connections of Q-cards, sliders, and smartphone detection systems are disclosed, described, and summarized herein in or listed in, or in, U.S. Provisional Application Nos. 62 / 456065, filed August 10, 2016 and September 14, 2016, respectively; U.S. Provisional Application Nos. 62 / 426065, filed February 7, 2017; and U.S. Provisional Application No. 62 / 456504, filed February 8, 2017, respectively, all of which are incorporated herein by reference in their entirety for all purposes.

[0924] In some implementations of QMAX, the sample contact area of ​​one or two plates includes a compression open flow monitoring surface structure (MSS) configured to monitor how much flow has occurred after COF. For example, in some implementations, the MSS comprises a shallow square array that will induce friction against components in the sample (e.g., blood cells in blood). By examining the distribution of some components in the sample, information related to the flow of the sample and its components under COF can be obtained.

[0925] The depth of the MSS can be 1 / 1000, 1 / 100, 1 / 100, 1 / 5, 1 / 2 of the spacer height or within any two values, and it can be either protruding or perforated.

[0926] (5) Detection methods

[0927] The apparatus, systems, and methods disclosed herein may include or be used in various types of detection methods. Detection methods are disclosed, described, and summarized herein in PCT applications (designated U.S.) PCT / US2016 / 045437 and PCT / US0216 / 051775 filed August 10, 2016, and September 14, 2016, respectively; U.S. Provisional Application No. 62 / 456065 filed February 7, 2017; U.S. Provisional Application No. 62 / 426065 filed February 8, 2017; and U.S. Provisional Application No. 62 / 456504 filed February 8, 2017, the entire contents of all such applications are incorporated herein for all purposes.

[0928] (6) mark

[0929] The apparatus, systems, and methods disclosed herein can employ various types of markers for analyte detection. Markers are disclosed herein or listed, described, and summarized in PCT applications (designated U.S.) filed August 10, 2016 and September 14, 2016, respectively; U.S. Provisional Application No. 62 / 456065 filed February 7, 2017; U.S. Provisional Application No. 62 / 426065 filed February 8, 2017; and U.S. Provisional Application No. 62 / 456504 filed February 8, 2017, the entire contents of all such applications are incorporated herein for all purposes.

[0930] (7) Analytes

[0931] The apparatus, systems, and methods disclosed herein can be used to operate and detect a wide variety of analytes, including biomarkers. Analytes are disclosed, described, and summarized herein in PCT applications (designated U.S.) PCT / US2016 / 045437 and PCT / US0216 / 051775, filed August 10, 2016, and September 14, 2016, respectively; U.S. Provisional Application No. 62 / 456065, filed February 7, 2017; U.S. Provisional Application No. 62 / 426065, filed February 8, 2017; and U.S. Provisional Application No. 62 / 456504, filed February 8, 2017, the entire contents of all these applications are incorporated herein for all purposes.

[0932] (8) Applications (fields and samples)

[0933] The apparatus, systems, and methods disclosed herein can be used in a wide variety of applications (fields and examples). Applications are disclosed, described, and summarized herein in PCT applications (designated U.S.) filed August 10, 2016 and September 14, 2016, PCT / US2016 / 045437 and PCT / US0216 / 051775, respectively; U.S. Provisional Application No. 62 / 456065 filed February 7, 2017; U.S. Provisional Application No. 62 / 426065 filed February 8, 2017; and U.S. Provisional Application No. 62 / 456504 filed February 8, 2017, the entire contents of all these applications are incorporated herein for all purposes.

[0934] (9) Cloud

[0935] The apparatus, systems, and methods disclosed herein can utilize cloud technology for data transmission, storage, and / or analysis. Related cloud technologies are disclosed, described, and summarized herein in PCT applications (designated U.S.) PCT / US2016 / 045437 and PCT / US0216 / 051775 filed August 10, 2016, and September 14, 2016, respectively; U.S. Provisional Application No. 62 / 456065 filed February 7, 2017; U.S. Provisional Application No. 62 / 426065 filed February 8, 2017; and U.S. Provisional Application No. 62 / 456504 filed February 8, 2017, the entire contents of all such applications are incorporated herein for all purposes.

[0936] Other notes

[0937] Other embodiments of the inventive subject matter according to this disclosure are described in the following paragraphs.

[0938] It must be noted that, as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly indicates otherwise, such as when the word “single” is used. For example, reference to “analyte” includes a single analyte and multiple analytes, reference to “capture agent” includes a single capture agent and multiple capture agents, reference to “detector” includes a single detector and multiple detectors, and reference to “reagent” includes a single reagent and multiple reagents.

[0939] As used herein, the terms “adapter” and “construction” mean that an element, component, or other subject is designed and / or intended to perform a given function. Therefore, the use of the terms “adapter” and “construction” should not be construed as meaning that a given element, component, or other subject is simply “capable” of performing a given function. Similarly, a subject stated as constructed to perform a particular function may additionally or optionally be described as operable to perform that function.

[0940] As used herein, the phrases “for example,” “as an example,” and / or simply the terms “example” and “exemplary” when referring to one or more components, features, details, structures, embodiments, and / or methods according to this disclosure are intended to convey illustrative, non-exclusive examples of the components, features, details, structures, embodiments, and / or methods according to this disclosure. Therefore, the described components, features, details, structures, embodiments, and / or methods are not intended to be limiting, essential, or exclusive / exhaustive; and other components, features, details, structures, embodiments, and / or methods, including those that are structurally and / or functionally similar and / or equivalent, are also within the scope of this disclosure.

[0941] As used herein, the phrases “at least one” and “one or more” for a list of more than one entity refer to any one or more entities in the entity list, and are not limited to at least one of each and every entity specifically listed in the entity list. For example, “at least one of A and B” (or equivalently, “at least one of A or B”, or equivalently, “at least one of A and / or B”) could refer to A alone, B alone, or a combination of A and B.

[0942] As used herein, the term “and / or” placed between the first entity and the second entity refers to (1) the first entity, (2) the second entity, and (3) one of the first entity and the second entity. Multiple entities listed using “and / or” should be interpreted in the same way, i.e., “one or more” of the entities thus combined. Other entities may optionally exist besides those specifically identified by the “and / or” clause, whether related to or unrelated to those specifically identified.

[0943] When referring to numerical ranges herein, the invention includes embodiments that include endpoints, embodiments that exclude both endpoints, and embodiments that include one endpoint while excluding the other. It should be assumed that both endpoints are included unless otherwise stated. Furthermore, unless otherwise stated or obvious from the context and understanding by one of ordinary skill in the art.

[0944] Where any patent, patent application or other reference is incorporated herein by reference and (1) defines a term in a manner inconsistent with any unincorporated portion of this disclosure or other incorporated references and / or (2) otherwise is inconsistent with any unincorporated portion of this disclosure or other incorporated references, the unincorporated portion of this disclosure shall prevail, and the term or the disclosure in which it is incorporated shall prevail only with respect to the reference in which the term is defined and / or the disclosure in which it is incorporated originally existed.

[0945] Other implementation plans

[0946] It should be understood that although the invention has been described in conjunction with a detailed description of the invention, the foregoing description is intended to illustrate rather than limit the scope of the invention, which is defined by the scope of the appended claims.

Claims

1. An optical assembly for imaging a sample using a handheld imaging device having a light source, a single camera, and a computer processor, said optical assembly comprising: shell; Lenses are arranged to provide a field of view to the camera; A cavity within the housing is used to receive the sample and position the sample within the field of view of the camera, wherein the lens is positioned to receive light refracted by or emitted by the sample when it is within the field of view of the camera. as well as The lever inside the cavity, The lever includes at least one optical element and is configured to be movable between a first position and a second position, wherein (i) in the first position, the imaging device is capable of imaging the sample in a bright field mode, and (ii) in the second position, the imaging device is capable of imaging the sample in a fluorescence excitation mode. and The lever includes a first planar region extending along a first plane and a second planar region laterally shifted from the first planar region along a first direction and extending along a second plane, the first plane being arranged at a different height from the second plane along a second direction perpendicular to the first direction.

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