Rack identification system

Abstract

A slide holder determination system for a digital slide scanning device is disclosed. In one embodiment, a motor drives the slide holder toward an engagement surface at a known rate. The time elapsed until engagement can be used to detect the presence or absence of the slide holder and / or the height of the slide holder. In addition, one or more sensors can detect one or more features of the slide holder, and these features can be used to determine the presence or absence of the slide holder, whether the digital slide scanning device supports or does not support the use of the slide holder, the orientation of the slide holder, and / or the manufacturer and / or model of the slide holder.

Description

[0001] This application is a divisional application of the invention patent application with the application date of November 27, 2018, application number 201880070069.8, and invention name “Carrier Determination System”. Technical Field

[0002] The present invention generally relates to a digital slide scanning device (e.g., for use in pathology), and more specifically, to a device for determining the type (e.g., manufacturer, model, etc.) and / or orientation of a slide rack prior to scanning an individual glass slide by the digital slide scanning device. Background Art

[0003] Digital pathology is an image-based information environment enabled by computer technology that allows the management of information generated from physical slides. Digital pathology is enabled in part by virtual microscopy, which is the practice of scanning samples on physical glass slides and producing digital glass slide images that can be stored, viewed, managed, and analyzed on a computer monitor. With the ability to image entire glass slides, the field of digital pathology has exploded and is currently considered one of the most promising approaches in diagnostic medicine to achieve even better, faster, and cheaper diagnosis, prognosis, and prediction of major diseases such as cancer.

[0004] Glass slides handled by digital slide scanning devices are very fragile but valuable. Glass slides may be stored in a variety of different types of slide racks made by different manufacturers. The characteristics of an individual slide rack made by a first manufacturer may differ significantly from the characteristics of an individual slide rack made by a second manufacturer. This results in conventional digital slide scanners damaging glass slides. Therefore, there is a need for a system and method that overcomes these significant problems found in the conventional systems described above. Summary of the invention

[0005] Therefore, in one embodiment, a slide rack determination system is described herein that operates within a digital slide scanning device and confirms the type and orientation of a slide rack holding multiple glass slides before scanning individual glass slides on a scanning stage of the digital slide scanning device. The system may include a slide rack clamp device having a lower clamp and an upper clamp. The lower clamp engages the bottom surface of the slide rack. The lower clamp and the slide rack are then driven toward the upper clamp until the upper clamp engages the top surface of the slide rack. The lower clamp and the slide rack are driven at a known (e.g., constant) rate, and therefore, the time taken for the upper clamp to engage the top surface of the slide rack provides an indication of the height of the slide rack.

[0006] In one embodiment, the upper fixture includes a plurality of sensors. The sensors on the upper fixture can be positioned to sense unique characteristics of a slide rack from a given manufacturer. Thus, when the upper fixture engages the top surface of the slide rack, a triggered individual sensor or a specific combination of triggered sensors provides an indication of the manufacturer of the slide rack and also provides an indication of the orientation of the slide rack. It is noteworthy that many individual slide racks are apparently uniform, and it is therefore not uncommon to process slide racks upside down. However, for digital slide scanning purposes, it is necessary to process glass slides with the top surface facing up. Therefore, advantageously, the slide rack determination system can be configured to determine the inverted orientation of the slide rack and generate an alarm, which will cause the slide rack to not be processed by the digital slide scanning device.

[0007] In one embodiment, a slide rack determination system is disclosed, the slide rack determination system comprising: a slide rack engagement surface, the slide rack engagement surface is configured to engage an engagement surface of a slide rack during processing of the slide rack by a digital slide scanning device; one or more sensors, the one or more sensors are configured to sense at least one feature of the slide rack when the engagement surface of the slide rack engages the slide rack engagement surface; and at least one hardware processor, the at least one hardware processor is configured to: receive output from the one or more sensors, and identify the slide rack based on the received output. Identification of the slide rack may include identifying a manufacturer of the slide rack, identifying a model of the slide rack, and / or determining whether the digital slide scanning device supports use of the slide rack.

[0008] The at least one hardware processor may be configured to determine the orientation of the carrier based on the received output. Additionally, the at least one hardware processor may be configured to: determine whether the orientation of the carrier is improper based on the received output from the one or more sensors; and when it is determined that the orientation of the carrier is improper, initiate an alarm to alert an operator that the orientation of the carrier is improper. The improper orientation of the carrier may be determined when the orientation of the carrier is inverted.

[0009] In one embodiment, the carrier identification system further comprises a motor configured to drive the carrier toward the carrier engagement surface along a linear axis within the digital carrier scanning device, wherein at least one of the one or more sensors is configured to sense engagement between the carrier engagement surface and the engagement surface of the carrier, and wherein the at least one hardware processor is further configured to activate the motor and deactivate the motor based on an output from the at least one sensor. The at least one hardware processor may be configured to: determine a time period between activation of the motor and the engagement between the carrier engagement surface and the engagement surface of the carrier; and determine a height of the carrier based on the time period; wherein the identification of the carrier is further based on the determined height of the carrier.

[0010] The at least one feature may include a feature on a side of the carrier, wherein the side is orthogonal to the engagement surface of the carrier. Alternatively or additionally, the at least one feature may include a feature on a peripheral edge of the engagement surface of the carrier. The one or more sensors may include a plurality of sensors configured to sense a plurality of features of the carrier, wherein the outputs from the plurality of sensors include indications of the plurality of features, and wherein identifying the carrier based on the received outputs from the plurality of sensors includes identifying all of the carriers that uniquely correspond to the indications of the plurality of features.

[0011] In one embodiment, the slide rack determination system is included in a digital slide scanning device. In such an embodiment, the at least one hardware processor may be configured to control the operation of a scanning process in the digital slide scanning device based on the identification of the slide rack.

[0012] In one embodiment, a method is disclosed, the method comprising at least one hardware processor of a digital slide scanning device: receiving output from one or more sensors, the one or more sensors being configured to sense at least one feature of the slide rack when an engagement surface of the slide rack engages with a slide rack engagement surface of the digital slide scanning device; and identifying the slide rack based on the received output from the one or more sensors.

[0013] Other features and advantages of the present invention will become more apparent to those of ordinary skill in the art after reading the following detailed description and accompanying drawings. BRIEF DESCRIPTION OF THE DRAWINGS

[0014] The structure and operation of the present invention will be understood by reading the following detailed description and accompanying drawings, in which like reference numerals refer to like parts and in which:

[0015] Figure 1A is a top view showing an example slide rack with glass slides from a first manufacturer according to one embodiment;

[0016] Figure 1B is a top view showing an example slide rack with glass slides from a second manufacturer according to one embodiment;

[0017] Figure 2A is a perspective view of an example slide holder from a first manufacturer shown engaged with an upper clamp according to one embodiment;

[0018] Figure 2B is a perspective view of an example slide holder from a second manufacturer shown engaged with an upper clamp according to one embodiment;

[0019] Figure 3 is a flow chart illustrating an example process for identifying the presence, orientation, characteristics, manufacturer and / or model of a slide rack, according to one embodiment;

[0020] Figure 4A is a block diagram illustrating an example processor-supporting device that may be used in conjunction with various embodiments described herein;

[0021] Figure 4B is a block diagram illustrating an example line scan camera having a single linear array, according to one embodiment;

[0022] Figure 4C is a block diagram showing an example line scan camera having three linear arrays, according to one embodiment; and

[0023] Figure 4D is a block diagram illustrating an example line scan camera having multiple linear arrays, according to one embodiment. DETAILED DESCRIPTION

[0024] Certain embodiments disclosed herein provide a slide rack determination system that determines the height and / or other features, manufacturer and / or model and / or orientation of a slide rack being processed by a digital slide scanning device. After reading this specification, it will become apparent to those skilled in the art how to implement the present invention in various optional embodiments and optional applications. However, although various embodiments of the present invention will be described herein, it should be understood that these embodiments are presented by way of example only and are not intended to be limiting. As such, this detailed description of various optional embodiments should not be construed as limiting the scope or breadth of the present invention as set forth in the appended claims.

[0025] 1. Example Slide Rack Determination System

[0026] Figure 1A is a top view showing an example slide holder 100A from a first manufacturer having a glass slide 585, according to one embodiment. In the illustrated embodiment, the slide holder 100A includes one or more slide holder features 120A-120E detectable by a sensor, including two recesses 120A and 120B in a top surface 110A of the slide holder 100A.

[0027] Figure 1B is a top view showing an example slide holder 100B from a second manufacturer having a glass slide 585, according to one embodiment. In the illustrated embodiment, the slide holder 100B includes one or more slide holder features 120F through 120J detectable by a sensor, including a single recess 120F in a top surface 110B of the slide holder 100B.

[0028] The rack features 120 may include: a ridge or other protrusion at a specific location from the surface of the rack 100; a notch, opening or other recess at a specific location in the surface of the rack 100; the presence of the surface of the rack 100 at a specific location; the absence of the surface of the rack 100 at a specific location, etc. In one embodiment, a single rack feature 120 may be used to uniquely identify a specific rack 100. Alternatively, a combination of multiple rack features 120 may be used collectively to uniquely identify a specific rack 100. Since a large portion of the top surface 110 of the rack 100 may be covered when the rack 100 is engaged with the rack engagement surface of the fixture (e.g., the upper fixture 200), it is preferred to use rack features 120 on the side of the rack 100 or near the peripheral edge of the top surface 110 of the rack 100 for easier detection.

[0029] Figure 2A is a perspective view of an example carrier 100A from a first manufacturer shown engaged with a carrier engagement surface (eg, bottom surface) of an upper fixture 200, according to one embodiment. Similarly, Figure 2B is a perspective view of an example carrier 100B from a second manufacturer shown engaged with a carrier engagement surface of an upper fixture 200, according to one embodiment.

[0030] A plurality of sensors 210 and 220 are attached to the upper fixture 200. The plurality of sensors may include one or more carrier orientation sensors 210 and one or more carrier feature sensors 220. In the illustrated embodiment, the plurality of sensors includes a single carrier orientation sensor 210 and two carrier feature sensors 220A and 220B. Additionally, at least one and / or another of the plurality of sensors 210 and / or 220 may be configured to determine whether the carrier 100 is engaged with the carrier engagement surface of the upper fixture 200. In alternative embodiments, additional or fewer sensors may be employed.

[0031] In one embodiment, each carrier orientation sensor 210 is configured to sense a carrier feature 120 that indicates whether the carrier 100 is topside up or upside down. Each carrier orientation sensor 210 may be specific to a single type of carrier 100 (e.g., 100A), or may be configured to determine the orientation of two or more types of carriers 100 (e.g., 100A and 100B).

[0032] In one embodiment, each rack feature sensor 220 is configured to determine the presence or absence of at least one rack feature 120. In one embodiment of identifying the manufacturer and / or model of a rack 100 based on multiple rack features 120, two or more rack feature sensors 220 (e.g., in the illustrated embodiment, 220A and 220B) may be used to determine which of multiple manufacturers manufactured the rack 100 and / or which of multiple models are present. Specifically, the combined outputs of the rack feature sensors 220 may be used to uniquely identify each manufacturer's rack 100 and / or each model of rack 100, with each combined output representing the presence or absence of a particular rack feature 120 and / or one or more parameters of a particular rack feature 120 (e.g., height, width, depth, thickness, shape, diameter, etc.). For example, the presence of a first carrier feature 120 (e.g., 120E) and / or the presence of a second carrier feature 120 (e.g., 120H) may indicate the presence of a carrier 100A from a first manufacturer, whereas the absence of the first carrier feature 120 and / or the presence of the second carrier feature 120 may indicate the presence of a carrier 100B from a second manufacturer.

[0033] In one embodiment, the digital slide scanning device includes a processor 555 that monitors each output of the slide rack orientation sensor 210 during slide processing and analyzes the output to determine the orientation of the slide rack 100 based on the output of the slide rack orientation sensor 210. In the case where the determination is performed based on the outputs from multiple slide rack orientation sensors 210, the processor 555 monitors multiple outputs of these slide rack orientation sensors 210 before and / or during slide processing. During the monitoring, if the processor 555 determines that the position of the slide rack 100 has become abnormal based on the output of the slide rack orientation sensor 210, then the processor 555 can trigger an alarm (e.g., an audio alarm via a speaker of the digital slide scanning device and / or a visual alarm via a display or light source of the digital slide scanning device) to alert the operator of the digital slide scanning device that the slide rack 100 is abnormally positioned. The processor 555 can also stop any slide processing until the slide rack 100 is repositioned, so that the processor 555 determines that the slide rack 100 is properly positioned based on the output of the slide rack orientation sensor 210.

[0034] Additionally or alternatively, the processor 555 of the digital slide scanning device receives each output of the rack characteristic sensor 220 and analyzes the output to determine the presence or absence of the rack 100 and / or if it is determined that the rack 100 is present, to uniquely identify the manufacturer, model and / or other type of the rack 100 and / or to determine whether the digital slide scanning device supports the use of the rack 100. If the processor 555 determines that the digital slide scanning device does not support the use of the rack 100, then the processor 555 may prevent any slide handling in order to prevent damage to the glass slides 585 within the rack 100, the rack 100 and / or the digital slide scanning device.

[0035] 2. Example Slide Rack Determination Process

[0036] Figure 3 is a flow chart illustrating a process 300 for identifying the presence, orientation, characteristics, manufacturer, and / or model of a slide rack 100, according to one embodiment. Although process 300 is illustrated as having a certain arrangement and order of steps, process 300 may be implemented with fewer, more, or different steps, and with different arrangements and / or orders of steps. Process 300 may be implemented by a digital slide scanning device, such as, Figure 4A The scanning system 550 shown is implemented by a processor 555.

[0037] The process 300 begins in step 310 when the motor begins to drive the carrier 100 so that the engagement surface 110 (e.g., the top surface) of the carrier 100 moves toward the carrier engagement surface (e.g., the bottom surface) of the fixture 200. For example, another engagement surface (e.g., the bottom surface) of the carrier 100 can rest on the carrier engagement surface (e.g., the top surface) of the lower fixture. The lower fixture can include a sensor to detect the presence of the carrier 100, and the processor 555 can automatically activate the motor to drive the lower fixture toward the upper fixture 200 whenever the sensor detects the presence of the carrier 100. Alternatively, the operator can manually activate the motor under the control of the controller 555 to drive the lower fixture toward the upper fixture 200.

[0038] In addition, in step 310, the processor 555 may begin monitoring the time from the activation time of the motor until the engagement time at which the engagement surface 110 of the carrier 100 engages with the carrier engagement surface of the upper clamp 200. For example, the processor 555 may start a timer at the activation time to stop it at the engagement time. Alternatively, the processor 555 may store the activation time at which the motor is activated and continuously compare the activation time with the current time (e.g., until the engagement time).

[0039] In step 320, the processor 555 monitors the output of the engagement sensor (e.g., sensor 210, 220, or another sensor) of the upper clamp 200. If the engagement sensor detects the carrier 100, it outputs a detection indication to the processor 555. Otherwise, if the engagement sensor does not detect the carrier, it outputs no indication or a no detection indication to the processor 555. If the processor 555 receives a detection indication (i.e., "yes" in step 320), the process 300 proceeds to step 350. Otherwise, if the processor 555 does not receive a detection indication or receives a no detection indication (i.e., "no" in step 320), the process 300 proceeds to step 330.

[0040] In step 330, the processor 555 determines whether the time period from the activation time in step 310 to the current time is greater than a threshold value. The threshold value may be set to indicate the length of time that there is no carrier 100 between the upper fixture and the lower fixture or indicates another error. If the length of time is greater than the threshold value (i.e., "yes" in step 330), then in step 340, the processor 555 may sound an alarm (e.g., an audio and / or visual alarm) to notify the operator that an error has been encountered. The alarm may include an indication of an error (e.g., the absence of a carrier 100). Otherwise, if the length of time is not greater than the threshold value (i.e., "no" in step 330), then in step 320, the process 300 may continue to monitor engagement. It should be understood that if the length of time is equal to the threshold value, then the processor 555 may sound an alarm or continue to step 320, depending on the specific design choice of the programmer.

[0041] In alternative embodiments, the processor 555 may utilize other means to detect the absence of the carrier 100. In this case, step 310 may omit starting the engagement timing and step 330 may be omitted entirely. As an example, the absence of the carrier 100 may be detected by sensing that the engagement surface of the lower clamp is within a predetermined distance from the engagement surface of the upper clamp or has reached the engagement surface of the upper clamp.

[0042] In step 350, the processor 555 may determine the height of the carrier 100. In one embodiment, the height of the carrier 100 is calculated based on a time period from the activation time in step 310 to the engagement time detected in step 320. For example, the height of the carrier 100 may be calculated based on the time period and a known constant speed of the motor activated in step 310 (e.g., height=speed×time period). Alternatively, the height of the carrier 100 may be determined based on the distance between the lower clamp and the upper clamp 200 at the time of engagement detected in step 320. It should be understood that the height of the carrier 100 may be used as a feature for identifying the manufacturer and / or model of the carrier 100. In an embodiment where the height of the carrier 100 is not required to identify the manufacturer of the carrier 100, step 350 may be omitted.

[0043] In step 360, the processor 55 may determine the orientation of the carrier 100. For example, the processor 555 may receive output from one or more carrier orientation sensors 210. Based on the output from the carrier orientation sensors 210, the processor may determine the orientation of the carrier 100. For example, the processor may determine whether the carrier 100 is topside up or upside down.

[0044] In step 370, if the orientation of the slide rack 100 is incorrect or inappropriate (e.g., "No" in step 370), then in step 340, the processor 555 may issue an alarm. For example, the incorrect or inappropriate orientation may include an upside-down orientation of the slide rack 100. The alarm may include an indication of an error (e.g., an inappropriate orientation of the slide rack 100). Otherwise, if the orientation of the slide rack 100 is correct and appropriate (i.e., "Yes" in step 370), then the process 300 proceeds to step 380.

[0045] In step 380, processor 555 may detect one or more features of carrier 100. For example, processor 555 may receive output from one or more carrier feature sensors 220. Based on the output from carrier feature sensors 220 and / or other detected features (e.g., the height of the carrier determined in step 350), processor 555 may identify carrier 100 in step 390.

[0046] Specifically, in step 390, the processor 555 may identify the manufacturer and / or model of the slide rack 100. This identification may then be used for further processing by the digital slide scanning device 550. For example, the identification of the manufacturer and / or model of the slide rack 100 may be used to determine whether the digital slide scanning device 550 supports the slide rack 100, to configure the operation of the digital slide scanning device 550 (such as the operation of the control assembly for loading and unloading slides 585 into and from the slide rack 100), etc.

[0047] 3. Example Implementation

[0048] In one embodiment, a rack identification system includes a rack engagement surface configured to engage a top surface of a rack during processing of the rack by a digital slide scanning device. The rack identification system also includes at least one sensor configured to sense at least one feature of the rack when the rack engages the rack engagement surface. The rack identification system also includes a processor configured to receive one or more indications from the at least one sensor and analyze the received one or more indications to determine a manufacturer of the rack.

[0049] In one embodiment, a rack determination system includes a rack engagement surface configured to engage a top surface of a rack during processing of the rack by a digital slide scanning device. The rack determination system also includes at least one sensor configured to sense at least one feature of the rack when the rack engages the rack engagement surface. The rack determination system also includes a processor configured to receive one or more indications from the at least one sensor and analyze the received one or more indications to determine an orientation of the rack.

[0050] In one embodiment, a rack determination system includes a motor configured to drive a rack along a linear axis within a digital slide scanning device, wherein the motor begins driving the rack at a first time. The rack determination system also includes a rack engagement surface located along the linear axis and configured to engage a top surface of the rack during processing of the rack by the digital slide scanning device. The rack determination system also includes at least one sensor configured to sense the engagement of the rack with the rack engagement surface, wherein the rack engages the rack engagement surface at a second time. The rack determination system also includes a processor configured to drive the motor, the processor further configured to determine the first time based on the start time of driving the motor, the processor further configured to receive an indication from the at least one sensor confirming the engagement of the rack with the rack engagement surface, the processor further configured to determine the second time based on the received indication, and the processor further configured to determine a height of the rack based on the first time and the second time. Similarly, the processor may determine the absence of a carrier based on an amount of time that has passed after the first time, such that if the processor drives the motor longer than a predetermined amount of time, the processor determines the absence of a carrier.

[0051] In one embodiment, a method for determining a carrier includes: driving a carrier toward a carrier engagement surface including a plurality of sensors; and after engaging a top surface of the carrier with the carrier engagement surface, receiving an indication from one or more sensors. The method also includes: analyzing the indication from the one or more sensors; and determining a carrier manufacturer based on the analysis.

[0052] In one embodiment, a method for determining a carrier includes: driving a carrier toward a carrier engagement surface including a plurality of sensors; and after engaging a top surface of the carrier with the carrier engagement surface, receiving an indication from one or more sensors. The method also includes: analyzing the indication from the one or more sensors; and determining a carrier orientation based on the analysis.

[0053] In one embodiment, a method includes: using a motor to drive a carrier toward a carrier engagement surface including a plurality of sensors; and storing a first time corresponding to when the motor begins to drive the carrier. The method also includes: sensing engagement of the carrier with the carrier engagement surface; and storing a second time corresponding to when the carrier engages the carrier engagement surface; and determining a carrier height based on an analysis.

[0054] 4. Example Digital Slide Scanning Device

[0055] Figure 4A 5 is a block diagram illustrating an example processor-supported apparatus 550 that may be used in conjunction with the various embodiments described herein. As will be appreciated by the skilled artisan, alternative forms of apparatus 550 may also be used. In the illustrated embodiment, the device 550 is presented as a digital imaging device (also referred to as a digital slide scanning apparatus, digital slide scanner, scanner, scanner system, digital imaging device, etc.), which includes: one or more processors 555; one or more memories 565; one or more motion controllers 570; one or more interface systems 575; one or more movable stages 580, each of which supports one or more glass slides 585 with one or more samples 590; one or more illumination systems 595, which illuminate the samples; one or more objective lenses 600, each of which defines an optical path 605 that travels along an optical axis; one or more objective lens positioners 630; one or more optional epi-illumination systems 635 (for example, included in a fluorescence scanner system); one or more focusing optical devices 610; one or more line scan cameras 615; and / or one or more area scan cameras 620, each of which defines a separate field of view 625 on the sample 590 and / or the glass slide 585. The various elements of the scanner system 550 are communicatively coupled via one or more communication buses 560. Although there may be one or more of each of the various elements of the scanner system 550, for simplicity of description, these elements will be described in the singular unless description in the plural is necessary to convey the appropriate information.

[0056] The one or more processors 555 may include, for example, a central processing unit (CPU) and a separate graphics processing unit (GPU) capable of processing instructions in parallel, or the one or more processors 555 may include a multi-core processor capable of processing instructions in parallel. Additional separate processors may also be provided to control specific components or perform specific functions, such as image processing. For example, additional processors may include auxiliary processors for managing data input, auxiliary processors for performing floating-point mathematical operations, special processors (e.g., digital signal processors) with an architecture suitable for quickly executing signal processing algorithms, slave processors (e.g., back-end processors) subordinate to the main processor, additional processors for controlling the line scan camera 615, the stage 580, the objective lens 225, and / or a display (not shown). Such additional processors may be separate discrete processors, or may be integrated with the processor 555. One or more processors can be configured to control a motor that drives the lower clamp and also configured to receive indications from one or more sensors attached to the upper clamp 200 and thereby control the overall workflow of the digital imaging device 550 and determine the height, manufacturer and / or orientation of the slide rack 100 being processed by the digital imaging device 550.

[0057] The memory 565 provides storage of data and instructions for programs that can be executed by the processor 555. The memory 565 may include one or more volatile and / or non-volatile computer-readable storage media that store data and instructions, including, for example, random access memory, read-only memory, hard disk drives, removable storage device drives, etc. The processor 555 is configured to execute the instructions stored in the memory 565 and communicate with the various elements of the scanner system 550 via the communication bus 560 to implement the overall functionality of the scanner system 550.

[0058] The one or more communication buses 560 may include a communication bus 560 configured to communicate analog electrical signals, and may include a communication bus 560 configured to communicate digital data. Thus, communications from the processor 555, motion controller 570, and / or interface system 575 via the one or more communication buses 560 may include both electrical signals and digital data. The processor 555, motion controller 570, and / or interface system 575 may also be configured to communicate with one or more of the various elements of the scanning system 550 via a wireless communication link.

[0059] The motion control system 570 is configured to precisely control and coordinate the XYZ movement of the stage 580 and the objective 600 (e.g., via the objective positioner 630). The motion control system 570 is also configured to control the movement of any other moving parts in the scanner system 550. For example, in a fluorescence scanner embodiment, the motion control system 570 is configured to coordinate the movement of filters in the epi-illumination system 635, etc.

[0060] The interface system 575 allows the scanner system 550 to interface with other systems and human operators. For example, the interface system 575 may include a user interface for providing information directly to an operator and / or allowing direct input from an operator. The interface system 575 is also configured to facilitate communication and data transfer between the scanner system 550 and one or more external devices (e.g., printers, removable storage media, etc.) connected directly or connected to the scanner system 550 via a network (not shown), such as an image server system, an operator station, a user station, and a management server system.

[0061] The illumination system 595 is configured to illuminate a portion of the sample 590. The illumination system 595 may include, for example, a light source and an illumination optic. The light source may be a variable intensity halogen light source having a concave reflector to maximize light output and having a KG-1 filter to suppress heat. The light source may also be an arc lamp, a laser, or other light source of any type. In one embodiment, the illumination system 595 illuminates the sample 590 in a transmission mode so that the line scan camera 615 and / or the surface scan camera 620 sense the optical energy transmitted through the sample 590. Alternatively or additionally, the illumination system 595 may be configured to illuminate the sample 590 in a reflection mode so that the line scan camera 615 and / or the surface scan camera 620 sense the optical energy reflected from the sample 590. In general, the illumination system 595 is configured to be suitable for interrogating the microscope sample 590 in any known mode of optical microscopy.

[0062] In one embodiment, the scanner system 550 optionally includes an epi-illumination system 635 to optimize the scanner system 550 for fluorescence scanning. Fluorescence scanning is the scanning of a sample 590 including fluorescent molecules, which are photon-sensitive molecules that can absorb light of a specific wavelength (excitation). These photon-sensitive molecules also emit light at a higher wavelength (emission). Since the efficiency of this photoluminescence phenomenon is very low, the amount of emitted light is usually very low. This low amount of emitted light typically hinders conventional techniques (e.g., transmission mode microscopy) for scanning and digitizing samples 590. Advantageously, in an optional fluorescence scanner system embodiment of the scanner system 550, a line scan camera 615 (e.g., a time delay integration (TDI) line scan camera) including multiple linear sensor arrays is used to increase the sensitivity of the line scan camera to light by exposing the same area of ​​the sample 590 to each of the multiple linear sensor arrays of the line scan camera 615. This is particularly useful when scanning weak fluorescent samples with low emission light.

[0063] Thus, in the fluorescence scanner system embodiment, the line scan camera 615 is preferably a monochrome TDI line scan camera. Advantageously, monochrome images are desirable in fluorescence microscopy because they provide a more accurate representation of the actual signal from the various channels present on the sample. As will be appreciated by those skilled in the art, the fluorescent sample 590 may be labeled with a variety of fluorescent dyes that emit light at different wavelengths, also referred to as "channels."

[0064] Furthermore, since the low-end and high-end signal levels of various fluorescent samples present a wide spectrum of wavelengths to be sensed by the line scan camera 615, it is expected that the low-end and high-end signal levels that can be sensed by the line scan camera 615 are similarly wide. Therefore, in the fluorescence scanner embodiment, the line scan camera 615 used in the fluorescence scanning system 550 is a monochrome 10-bit 64 linear array TDI line scan camera. It should be noted that various bit depths of the line scan camera 615 can be employed for use with the fluorescence scanner embodiment of the scanning system 550.

[0065] The movable stage 580 is configured to perform precise XY axis movement under the control of the processor 555 or the motion controller 570. The movable stage can also be configured to move in the Z axis under the control of the processor 555 or the motion controller 570. The movable stage is configured to position the sample at a desired position during image data capture by the line scan camera 615 and / or the area scan camera. The movable stage is also configured to accelerate the sample 590 to a substantially constant speed in the scanning direction, and then maintain a substantially constant speed during image data capture by the line scan camera 615. In one embodiment, the scanner system 550 can use a high-precision and tightly coordinated XY grid to help position the sample 590 on the movable stage 580. In one embodiment, the movable stage 580 is an XY stage based on a linear motor, wherein high-precision encoders are used on both the X-axis and the Y-axis. For example, very precise nano encoders can be used on the axis in the scanning direction and on the axis in the direction perpendicular to the scanning direction and in the same plane as the scanning direction. The stage is also configured to support a glass slide 585 on which a sample 590 is disposed.

[0066] Sample 590 can be anything that can be interrogated by optical microscopy. For example, glass microscope slide 585 is often used as the observation substrate of sample, and this sample comprises tissue and cell, chromosome, DNA, protein, blood, bone marrow, urine, bacteria, droplet, biopsy material, or any other type of dead or alive, dyed or undyed, labeled or unlabeled biological material or substance. Sample 590 can also be any type of DNA or DNA related material (such as cDNA, RNA or protein) array deposited on any type of slide or other substrate, including any and all samples commonly referred to as microarray. Sample 590 can be microtiter plate, such as 96-well plate. Other examples of sample 590 include integrated circuit board, electrophoresis record, culture dish, membrane, semiconductor material, forensic material and machined parts.

[0067] The objective lens 600 is mounted on an objective lens positioner 630, which in one embodiment can employ a very precise linear motor to move the objective lens 600 along the optical axis defined by the objective lens 600. For example, the linear motor of the objective lens positioner 630 can include a 50 nanometer encoder. The relative positions of the stage 580 and the objective lens 600 in the XYZ axes are coordinated and controlled in a closed-loop manner using a motion controller 570 under the control of a processor 555, which employs a memory 565 to store information and instructions, including computer executable programming steps for the overall operation of the scanning system 550.

[0068] In one embodiment, objective 600 is a plan apochromatic ("APO") infinity-corrected objective having a numerical aperture corresponding to the highest desired spatial resolution, wherein objective 600 is suitable for transmission mode illumination microscopy, reflection mode illumination microscopy, and / or epi-illumination mode fluorescence microscopy (e.g., Olympus 40X, 0.75NA or 20X, 0.75NA). Advantageously, objective 600 is capable of correcting chromatic and spherical aberrations. Since objective 600 is infinity-corrected, focusing optics 610 can be placed above objective 600 in optical path 605, wherein a light beam passing through the objective becomes a collimated light beam. Focusing optics 610 focuses the light signal captured by objective 600 onto the light responsive elements of line scan camera 615 and / or area scan camera 620 and can include optical components (such as filters, magnification converter lenses, etc.). Objective 600 in combination with focusing optics 610 provides the overall magnification for scanning system 550. In one embodiment, focusing optics 610 may include a tube lens and an optional 2X magnification changer. Advantageously, the 2X magnification changer allows the native 20X objective 600 to scan sample 590 at 40X magnification.

[0069] The line scan camera 615 includes at least one linear array of picture elements ("pixels"). The line scan camera can be monochrome or color. A color line scan camera typically has at least three linear arrays, while a monochrome line scan camera can have a single linear array or multiple linear arrays. Any type of singular or plural linear array can also be used, whether packaged as part of the camera or custom integrated into the imaging electronics module. For example, a 3-linear array ("red-green-blue" or "RGB") color line scan camera or a 96-linear array monochrome TDI can also be used. TDI line scan cameras typically provide significantly better SNR in the output signal by summing the intensity data from previously imaged areas of the sample to produce an increase in the signal-to-noise ratio (SNR) proportional to the square root of the number of integration stages. A TDI line scan camera includes multiple linear arrays. For example, a TDI line scan camera can have 24, 32, 48, 64, 96 or even more linear arrays. The scanner system 550 also supports linear arrays manufactured in a variety of formats, including some formats with 512 pixels, some formats with 1,024 pixels, and other formats with up to 4,096 pixels. Similarly, linear arrays with various pixel sizes can also be used in the scanner system 550. A prominent requirement for selecting any type of line scan camera 615 is that the movement of the stage 580 can be synchronized with the line rate of the line scan camera 615 so that the stage 580 can be in motion relative to the line scan camera 615 during the capture of the digital image of the sample 590.

[0070] Image data generated by line scan camera 615 is stored in a portion of memory 565 and processed by processor 555 to generate a continuous digital image of at least a portion of sample 590. The continuous digital image can be further processed by processor 555, and the processed continuous digital image can also be stored in memory 565.

[0071] In an embodiment having two or more line scan cameras 615, at least one of the line scan cameras 615 can be configured to function as a focus sensor that operates in combination with at least one of the line scan cameras 615 that is configured to function as an imaging sensor. The focus sensor can be logically positioned on the same optical axis as the imaging sensor, or the focus sensor can be logically positioned before or after the imaging sensor relative to the scanning direction of the scanner system 550. In an embodiment in which at least one line scan camera 615 functions as a focus sensor, image data generated by the focus sensor is stored in a portion of the memory 565 and processed by one or more processors 555 to generate focus information, thereby allowing the scanner system 550 to adjust the relative distance between the sample 590 and the objective lens 600 to maintain focus on the sample during scanning. Additionally, in an embodiment, at least one line scan camera 615 that functions as a focus sensor can be oriented so that each of a plurality of individual pixels of the focus sensor is positioned at a different logical height along the optical path 605.

[0072] In operation, the various components of the scanner system 550 and the programmed modules stored in the memory 565 implement automatic scanning and digitization of a sample 590 disposed on a glass slide 585. The glass slide 585 is securely placed on the movable stage 580 of the scanner system 550 to scan the sample 590. Under the control of the processor 555, the movable stage 580 accelerates the sample 590 to a substantially constant speed for sensing by the line scan camera 615, wherein the speed of the stage is synchronized with the line rate of the line scan camera 615. After scanning the image data strip, the movable stage 580 decelerates and brings the sample 590 to a substantially complete stop. The movable stage 580 then moves orthogonally to the scan direction to position the sample 590 for scanning of subsequent image data strips (e.g., adjacent strips). Additional strips are subsequently scanned until an entire portion of the sample 590 or the entire sample 590 is scanned.

[0073] For example, during the digital scanning of sample 590, a continuous digital image of sample 590 is acquired as a plurality of continuous fields of view, which are combined together to form an image strip. A plurality of adjacent image strips are similarly combined together to form a continuous digital image of a portion of sample 590 or the entire sample 590. The scanning of sample 590 may include acquiring a vertical image strip or a horizontal image strip. The scanning of sample 590 may be from top to bottom, from bottom to top, or both (bidirectional), and may start at any point on the sample. Alternatively, the scanning of sample 590 may be from left to right, from right to left, or both (bidirectional), and may start at any point on the sample. Additionally, it is not necessary to acquire the image strips in an adjacent or continuous manner. In addition, the resulting image of sample 590 may be an image of the entire sample 590 or only a portion of sample 590.

[0074] In one embodiment, computer executable instructions (e.g., programmed modules or other software) are stored in memory 565 and, when executed, enable scanning system 550 to perform the various functions described herein. In this specification, the term "computer-readable storage medium" is used to refer to any medium for storing computer executable instructions and providing them to scanning system 550 for execution by processor 555. Examples of such media include memory 565 and any removable or external storage media (not shown) that is communicatively coupled (e.g., via a network) directly or indirectly to scanning system 550.

[0075] Figure 4B A line scan camera is shown having a single linear array 640, which can be implemented as a charge coupled device ("CCD") array. The single linear array 640 includes a plurality of individual pixels 645. In the illustrated embodiment, the single linear array 640 has 4,096 pixels. In alternative embodiments, the linear array 640 can have more or fewer pixels. For example, common formats for linear arrays include 512, 1,024, and 4,096 pixels. The pixels 645 are arranged in a linear manner to define a field of view 625 of the linear array 640. The size of the field of view varies depending on the magnification of the scanner system 550.

[0076] Figure 4C A line scan camera is shown with three linear arrays, each of which can be implemented as a CCD array. The three linear arrays are combined to form a color array 650. In one embodiment, each individual linear array in the color array 650 detects a different color intensity (e.g., red, green, or blue). The color image data from each individual linear array in the color array 650 is combined to form a single field of view 625 of color image data.

[0077] Figure 4D A line scan camera is shown having multiple linear arrays, each of which can be implemented as a CCD array. Multiple linear arrays are combined to form a TDI array 655. Advantageously, a TDI line scan camera can provide significantly better SNR in its output signal by summing intensity data from previously imaged areas of the sample, with an increase in SNR proportional to the square root of the number of linear arrays (also called integrating stages). A TDI line scan camera can include a greater number of linear arrays. For example, common formats for TDI line scan cameras include 24, 32, 48, 64, 96, 120 and even more linear arrays.

[0078] The above description of the disclosed embodiments is provided to enable any person skilled in the art to make or use the present invention. Various modifications to these embodiments will be apparent to those skilled in the art, and the general principles described herein may be applied to other embodiments without departing from the spirit or scope of the present invention. Therefore, it should be understood that the description and accompanying drawings presented herein represent the current preferred embodiments of the present invention, and therefore represent the subject matter broadly contemplated by the present invention. It should also be understood that the scope of the present invention fully encompasses other embodiments that may become apparent to those skilled in the art, and the scope of the present invention is accordingly not limited.

Claims

1. A slide rack determination system, the slide rack determination system comprising: a slide holder assembly having a lower holder and an upper holder configured to hold a slide holder and having a slide holder engagement surface configured to engage an engagement surface of the slide holder during processing of the slide holder by a digital slide scanning device; The lower clamp engages the slide holder; The lower fixture and the slide carrier are driven toward the upper fixture; one or more sensors on a carrier clamp device, the one or more sensors configured and positioned to sense at least one feature of the carrier when the engagement surface of the carrier engages the carrier engagement surface, the at least one feature comprising one or more protrusions or recesses at one or more locations on a side of the carrier or at a peripheral edge of a top surface of the carrier, such that the at least one feature identifies the carrier; as well as At least one hardware processor is configured to receive output from the one or more sensors and identify the slide rack based on the received output.

2. The slide rack identification system of claim 1, wherein identifying the slide rack comprises identifying a manufacturer of the slide rack.

3. The slide rack identification system of claim 1, wherein identifying the slide rack comprises identifying a model number of the slide rack.

4. The slide rack determination system of claim 1, wherein identifying the slide rack comprises determining whether the digital slide scanning device supports use of the slide rack.

5. The slide carrier determination system of claim 1, wherein the at least one hardware processor is further configured to determine an orientation of the slide carrier based on the received output.

6. The rack determination system of claim 1, wherein the at least one hardware processor is further configured to: determining, based on the received outputs from the one or more sensors, whether the orientation of the carrier is improper; and When it is determined that the orientation of the carrier is improper, an alarm is initiated to alert an operator that the orientation of the carrier is improper.

7. The slide rack determination system of claim 6, wherein the orientation of the slide rack is determined to be improper when the orientation of the slide rack is inverted.

8. The carrier identification system of claim 1, further comprising a motor configured to drive the carrier toward the carrier engagement surface along a linear axis within the digital carrier scanning device, wherein at least one of the one or more sensors is configured to sense engagement between the carrier engagement surface and the engagement surface of the carrier, and wherein the at least one hardware processor is further configured to activate the motor and deactivate the motor based on an output from the at least one sensor.

9. The slide carrier identification system of claim 1, wherein the at least one feature comprises a feature on a side of the slide carrier, wherein the side is orthogonal to the engagement surface of the slide carrier.

10. The carrier identification system of claim 1, wherein the at least one feature comprises a feature on a peripheral edge of the engagement surface of the carrier.

11. A carrier identification system as described in claim 1, wherein the one or more sensors include a plurality of sensors configured to sense multiple features of the carrier, wherein the outputs from the plurality of sensors include indications of the multiple features, and wherein identifying the carrier based on the received outputs from the plurality of sensors includes identifying all of the carriers that uniquely correspond to the indications of the multiple features.

12. A digital slide scanning device comprising the slide rack determination system according to claim 1.

13. The digital slide scanning device of claim 12, wherein the at least one hardware processor is further configured to control the operation of a scanning process in the digital slide scanning device based on the identification of the slide rack.

14. A method comprising, by at least one hardware processor of a digital slide scanning device: receiving output from one or more sensors located on a fixture assembly, the one or more sensors being configured to sense at least one feature of the carrier when an engagement surface of the carrier engages a carrier engagement surface on a fixture assembly of the digital slide scanning device; and The clamp device has a lower clamp and an upper clamp; The lower clamp engages the slide holder; The lower fixture and the slide carrier are driven toward the upper fixture; Based on the received output from the one or more sensors, the carrier rack is identified.

15. A slide rack determination system, comprising: Upper clamp; Lower clamp; a slide rack engagement surface of the upper fixture, wherein the slide rack is configured to engage an engagement surface of a slide rack that holds a plurality of glass slides during processing of the glass slides by a digital slide scanning device; The lower clamp engages the slide holder; The lower fixture and the slide carrier are driven toward the upper fixture; one or more sensors located on a portion of the upper fixture configured to sense at least one characteristic of the carrier when the carrier engagement surface engages the carrier engagement surface, wherein the at least one characteristic includes the presence or absence of the carrier at a particular location; and At least one hardware processor is configured to receive output from the one or more sensors and, based on the received output, identify the wafer carrier, wherein the at least one feature includes one or more protrusions or recesses on a side or top surface of the wafer carrier.

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