SYSTEM AND METHOD FOR TRACKING OBSERVATION POSITION DURING SAMPLE ANALYSIS - Patent application

Abstract

The sample analyzer is configured to acquire first and second stage position data. The first stage position data indicates a first position of the movable stage in a first dimension and the second stage position data indicates a second position of the movable stage in a second (vertical) dimension. The sample analyzer is configured to determine an observation position of one or more observation or imaging optics relative to the movable stage based on the first and second stage position data. The sample analyzer is configured to display a container map, the container map including a visual representation of the sample container associated with the movable stage. The sample analyzer is configured to display an observation position marker overlaid on the container map. The observation position marker indicates an observation position of the one or more observation or imaging optics relative to the sample container represented by the container map.

Description

[Technical field]

[0001] The present disclosure relates to the field of microscopy, and more particularly to systems and methods for tracking an observation position during an analysis. [Background technology]

[0002] Microscopy relates to observing small, often microscopic objects such as live cells. Live cell samples are often loaded into a sample container and then positioned on a microscope for observation and / or imaging. Some sample containers include sample wells to receive live cell samples and keep them separate from other live cell samples in the same sample container. To allow a user to observe different sample wells of a sample container, many microscopes are configured with a movable stage. After securing a sample container to the movable stage, a user can adjust the position of the movable stage to position a different sample well for observation / imaging through the microscope objective.

[0003] A sample container may contain a large sample area and / or a large number of wells, such as 96 or more wells. As a result, a user analyzing a sample with a microscope may lose track of which portion(s) of the sample container they are viewing and / or have already viewed, especially as the user repeatedly adjusts the microscope's movable stage during an imaging / analysis session. Such occurrences may reduce sample analysis efficiency and may prevent the user from remembering where structures of interest can be found within the sample container.

[0004] Thus, there is a continuing need and desire for improved systems and methods for tracking observation positions during sample analysis.

[0005] The subject matter claimed herein is not limited to embodiments that solve any shortcomings or that operate only in environments such as those described above. Rather, this background is only provided to illustrate one example technology area where some embodiments described herein may be practiced. Summary of the Invention

[0006] Implementations of the present disclosure extend to at least systems and methods for tracking observation positions during sample analysis.

[0007] Some embodiments provide a sample analyzer that includes a movable stage including a container holder configured to receive a sample container and a stage position adjuster configured to translate the movable stage in at least a first dimension and a second dimension perpendicular to the first dimension. The movable stage also includes a first position encoder configured to generate a first output indicative of a first position of the movable stage in the first dimension and a second position encoder configured to generate a second output indicative of a second position of the movable stage in the second dimension.

[0008] Some embodiments provide a sample analyzer including a display, one or more processors, and one or more hardware storage devices storing instructions executable by the one or more processors to configure the sample analyzer to perform operations. The operations include obtaining first and second stage position data. The first stage position data indicates a first position of a moveable stage in a first dimension, and the second stage position data indicates a second position of the moveable stage in a second dimension perpendicular to the first dimension. The operations further include determining an observation position of one or more viewing or imaging optics relative to the moveable stage based on the first and second stage position data. The operations further include displaying a container map on the display. The container map includes a visual representation of a sample container associated with the moveable stage. The operations further include displaying an observation position marker overlaid on the container map. The observation position marker indicates an observation position of one or more viewing or imaging optics relative to the sample container represented by the container map.

[0009] This Summary is provided to introduce a selection of concepts in a simplified form that are further described below in the Detailed Description. This Summary is not intended to identify key features or essential features of the claimed subject matter, nor is it intended to be used as an aid in determining the scope of the claimed subject matter.

[0010] Additional features and advantages will be set forth in the description which follows, and in part will be obvious from the description, or may be learned by the practice of the teachings herein. The features and advantages of the invention may be realized and obtained by means of the instruments and combinations particularly pointed out in the appended claims. The features of the invention will become more fully apparent from the following description and the appended claims, or may be learned by the practice of the invention as set forth hereinafter. [Brief description of the drawings]

[0011] To explain how the above-mentioned and other advantages and features can be obtained, a more particular description of the subject matter briefly described above will be rendered by reference to specific embodiments illustrated in the accompanying drawings, with the understanding that these drawings depict only typical embodiments and therefore should not be considered limiting in scope, the embodiments will be described and explained with additional specificity and detail through the use of the accompanying drawings. [Figure 1] 1 illustrates exemplary components of a sample analyzer according to an implementation of the present disclosure. [Diagram 2] 1 illustrates an example graphical user interface showing an observation position marker and a container map, according to an implementation of the present disclosure. [Diagram 3] 1 illustrates an example graphical user interface showing sample well identifiers associated with sample wells of a sample container, according to an implementation of the present disclosure. [Figure 4] 1 illustrates a conceptual diagram of saving viewing position according to an implementation of the present disclosure. [Diagram 5] 1 illustrates an example graphical user interface showing a container map, an observation location marker, and an observation location entry, according to an implementation of the present disclosure. [Figure 6] 1 illustrates an example graphical user interface showing a container map, an observation location marker, and an observation location entry, according to an implementation of the present disclosure. [Figure 7] 1 illustrates an example graphical user interface showing a container map, an observation location marker, and an observation location entry, according to an implementation of the present disclosure. [Figure 8] 1 shows an example flow diagram illustrating operations associated with tracking observation position during sample analysis, according to an implementation of the present disclosure. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0012] Implementations of the present disclosure extend to at least systems and methods for tracking observation positions during sample analysis.

[0013] Embodiments of the present disclosure may be implemented to address various shortcomings associated with at least some conventional sample analysis systems, which may include, but are not limited to, conventional microscope systems with movable stages with manual controls. For example, embodiments of the present disclosure may use one or more position encoders to obtain position data associated with a movable stage of a sample analyzer (e.g., a microscope system). The position data may be used to determine an observation position of an observation or imaging optics (e.g., an objective lens of a microscope system) relative to the movable stage (or relative to a sample container positioned within the movable stage). Embodiments of the present disclosure may display a container map corresponding to a sample container positioned on the movable stage, and an observation position marker may be displayed in combination with the container map to indicate the positioning of the observation or imaging optics relative to the sample container (as represented by the container map).

[0014] By displaying a container map (representing a sample container positioned on a movable microscope stage) in combination with an observation position marker (representing the observation position of the observation optics or imaging optics relative to the sample container), embodiments of the present disclosure can provide a user with an intuitive representation of the relative positioning between the microscope objective lens and various portions of the sample container positioned within the microscope. For example, the container map may include a visual representation of a sample well or other sample holding structure associated with a particular type of sample container positioned on the microscope stage. Thus, by displaying a container map in combination with an observation position marker, embodiments of the present disclosure can communicate to a user the observation position of the microscope objective lens relative to a particular sample well or other sample holding structure of the sample container. Thus, a user can avoid getting lost or disoriented when using a microscope with a movable stage to observe a sample.

[0015] At least some embodiments of the present disclosure are configured to include or perform operations such as saving viewing locations of interest, facilitating guided navigation to saved viewing locations of interest, displaying sample well markers and / or embedding sample well markers into captured image files, and / or others. Such embodiments may be implemented to further improve the user experience when using a microscope to analyze / capture samples.

[0016] Attention is now directed to Figures 1-8, which provide various supporting illustrations related to embodiments of the present disclosure.

[0017] Exemplary Systems and Techniques for Tracking Observation Position During Sample Analysis FIG. 1 illustrates various exemplary components of a sample analyzer 100 that may be used to implement one or more disclosed embodiments. While FIG. 1 illustrates the sample analyzer 100 including certain components, it will be understood in light of this disclosure that the sample analyzer 100 may include any number of additional or alternative components. Additionally, FIG. 1 illustrates the sample analyzer 100 as a microscope configured to perform cellular analysis. It will be understood in light of this disclosure that the principles disclosed herein are not limited to the particular configuration and / or characteristics of the sample analyzer 100 illustrated in FIG. 1. For example, the principles disclosed herein may be implemented in conjunction with any type of phase contrast, fluorescence, holotomography, and / or other microscopy system.

[0018] FIG. 1 shows that the sample analyzer 100 may include processor(s) 102, storage 104, input / output system(s) 110 (I / O system(s) 110), and communication system(s) 112. The processor(s) 102 may include one or more sets of electronic circuitry including any number of logic units, registers, and / or control units to facilitate execution of computer-readable instructions (e.g., instructions forming a computer program). Such computer-readable instructions may be stored in storage 104. Storage 104 may include physical system memory, and may be volatile, non-volatile, or some combination thereof. Additionally, storage 104 may include local storage, remote storage (e.g., accessible via communication system(s) 112, etc.), or some combination thereof. Additional details regarding the processor (e.g., processor(s) 102), computer storage media (e.g., storage 104), and other computer components are provided below.

[0019] The processor(s) 102 may be configured to execute instructions 106 stored in storage 104 to perform certain operations associated with tracking observation positions for sample analysis. The operations may depend at least in part on data 108 (e.g., stage position data, etc.) stored in storage 104 in a volatile or non-volatile manner.

[0020] In some examples, operations may rely at least in part on communication system(s) 112 to receive data from remote system(s) 114, which may include, for example, separate microscope systems, computing devices, sensors, and / or others. Communication system(s) 112 may include any combination of software or hardware components operable to facilitate communication between on-system components / devices and / or with off-system components / devices. For example, communication system(s) 112 may include ports, buses, or other physical connection devices for communicating with other devices / components. Additionally or alternatively, communication system(s) 112 may include systems / components operable to wirelessly communicate with external systems and / or devices through any suitable communication channel(s), such as, by way of non-limiting examples, Bluetooth, ultra-wideband, WLAN, infrared communication, etc.

[0021] 1 further illustrates that the sample analyzer 100 may include or be in communication with I / O system(s) 110. The I / O system(s) 110 may include any type of input or output device, such as, but not limited to, a display, a touch screen, a mouse, a keyboard or button interface, a controller, and / or others, as non-limiting examples.

[0022] FIG. 1 illustrates various additional components of the sample analyzer 100. For example, FIG. 1 illustrates a vessel holder 116 on a movable stage 118. The vessel holder 116 is configured to receive a sample vessel, such as a sample vessel for receiving and holding a live / dead cell sample for analysis using the sample analyzer 100. As described above, the sample vessel may comprise a sample slide and / or one or more sample wells for receiving the sample. Non-limiting examples of sample vessel configurations include 1-slide, 2-slide, 6-well, 12-well, 24-well, 48-well, 96-well, 384-well, and / or others. In some implementations, the vessel holder 116 includes a retaining member (e.g., a side-pushing retaining clip or other biasing member) that retains the sample vessel in a final position within the vessel holder 116, thereby securing the sample vessel relative to the movable stage 118.

[0023] In some implementations, the movable stage 118 of the sample analyzer 100 is positionable to facilitate imaging of different portions of a sample container held within the movable stage container holder 116. In this regard, the sample analyzer 100 may include a stage position adjuster configured to translate the movable stage 118 in at least two dimensions (e.g., an x-dimension and a y-dimension perpendicular to the x-dimension). In the example shown in FIG. 1, the sample analyzer 100 includes an x-adjustment knob 120 and a y-adjustment knob 122. The x-adjustment knob 120 is rotatable to facilitate planar translation of the movable stage 118 in a first direction / dimension (e.g., front-to-back), while the y-adjustment knob 122 is rotatable to facilitate planar translation of the movable stage 118 in a second direction / dimension (e.g., left-to-right) perpendicular to the first direction / dimension.

[0024] In light of the present disclosure, it should be understood that the particular hardware configuration of the stage position adjuster of the sample analyzer 100 of Figure 1 is provided by way of example only and is non-limiting. For example, one or more components of the movable stage 118 may be adjustable utilizing one or more sliders or other adjustment components. Additionally, while the movable stage 118 of the sample analyzer 100 of Figure 1 is adjustable by user manipulation of the physical elements of the sample analyzer, the movable stage 118 of the sample analyzer may also be adjusted by one or more motor systems that are electrically driven (e.g., to additionally or alternatively facilitate automated stage position adjustment based on input commands).

[0025] The example sample analyzer 100 of Figure 1 also includes position tracking sensors. In particular, Figure 1 shows a first position encoder 124 and a second position encoder 126. The first position encoder 124 is configured to generate a sensor output indicative of a position (or change in position) of the moveable stage 118 in a first direction / dimension (e.g., the x-dimension), and the second position encoder 126 is configured to generate a sensor output indicative of a position (or change in position) of the moveable stage in a second direction / dimension (e.g., the y-dimension). In this manner, as the positioning of the moveable stage 118 is adjusted (e.g., using the x-adjustment knob 120 and / or the y-adjustment knob 122), the first position encoder 124 and the second position encoder 126 provide outputs that facilitate tracking of the updated position of the moveable stage 118.

[0026] The first position encoder 124 and / or the second position encoder 126 can take a variety of forms. For example, in some implementations, the first position encoder 124 and / or the second position encoder 126 comprise an incremental encoder that outputs sensor data indicative of a change in position (e.g., a translation distance). When an incremental encoder is used, to facilitate consistent position tracking between power cycles of the sample analyzer 100, a calibration step may be performed between power cycles by moving (or instructing a user to move) the movable stage 118 to a known reference or starting position (e.g., a particular angular position). After moving the movable stage 118 to the known position, the change in position detected by the incremental encoder may be applied to the initial or previous positioning of the movable stage 118 to determine an updated position of the movable stage 118.

[0027] In some implementations, the first position encoder 124 and / or the second position encoder 126 comprise absolute encoders that output sensor data indicative of an absolute position. For example, the position outputs of the absolute encoders may be correlated one-to-one with specific stage positions such that each position output of the absolute encoder indicates a respective specific stage position (in each dimension). In such implementations, consistent stage position tracking may be achieved without performing a calibration step between each power cycle of the sample analyzer 100.

[0028] In some implementations, the first position encoder 124 and / or the second position encoder 126 are implemented as linear encoders. For example, the example of FIG. 1 illustrates the first position encoder 124 and the second position encoder 126 as including respective linear elements extending along first and second dimensions (e.g., x- and y-dimensions). These linear elements can comprise features detectable by corresponding sensors and indicative of a particular position or change in position (when detected by the corresponding sensors). While the encoder components illustrated in FIG. 1 are mounted externally to the sample analyzer 100, it should be understood in light of the present disclosure that such components may also be mounted internally to the sample analyzer 100.

[0029] In some implementations, the first position encoder 124 and / or the second position encoder 126 are implemented as rotary encoders and thus are positioned on or within rotatable elements (e.g., x-adjustment knob 120 and y-adjustment knob 122) associated with the translation of the moveable stage 118. Whether implemented as linear or rotary encoders, the first position encoder 124 and / or the second position encoder 126 may comprise magnetic encoders, optical encoders, capacitive encoders, and / or others.

[0030] 1 further illustrates the objective lens 128 of the sample analyzer 100. The objective lens 128 comprises one or more lenses configured to focus light reflected or scattered from the sample to form an image on a detector (e.g., an image sensor or a human eye). For example, as described above, a user can adjust the position of the movable stage 118 when a sample container is positioned thereon to move a region of interest of the sample container over the objective lens 128. The illuminator of the sample analyzer 100 may emit light that is directed by the collector 136 onto the region of interest of the sample container, and the light may scatter or reflect from the region of interest towards the objective lens 128 for imaging / detection.

[0031] The focus position of the objective lens 128 shown in Figure 1 is adjustable via focus knobs 130 and 132. In some examples, the sample analyzer 100 includes multiple objective lenses, which may be selected via an objective lens selection wheel 134 or other similar device for switching between objective lenses (e.g., a lens slider). In light of the present disclosure, it should be understood that the sample analyzer 100 may include any number of optics, filters, detectors, focusers, illuminators, and / or other components to facilitate imaging and / or image capture of a sample.

[0032] FIG. 1 further illustrates the sample analyzer 100 as including or in communication with a display 138. The particular type and form of the display 138 illustrated in FIG. 1 is not limiting of the present disclosure. The processor(s) 102 may execute instructions 106 operable to cause one or more graphical user interfaces and / or other visual elements to be presented on the display 138. For example, a captured image of a sample acquired by the sample analyzer 100 may be presented on the display 138 in response to execution of the instructions 106 by the processor(s) 102. As described in more detail below, a visual representation of an observation position relative to a sample container may be generated and / or presented on the display 138 to facilitate observation position tracking.

[0033] FIG. 2 illustrates an exemplary graphical user interface 200 showing an observation position marker 212 and a vessel map 204, according to an implementation of the present disclosure. The graphical user interface 200 may be generated or rendered in response to execution of instructions 106 using the processor(s) 102. FIG. 2 conceptually illustrates a vessel type selection 202, which may be obtained automatically or based on user input. For example, a user may place a sample vessel on a vessel holder 116 of a movable stage 118 of the sample analyzer 100 and provide user input at the sample analyzer (e.g., via the I / O system(s) 110) indicating a vessel type associated with the sample vessel. For example, in response to a user interface prompt, the user may select from available vessel types including 1-slide, 2-slide, 6-well, 12-well, 24-well, 48-well, 96-well, 384-well, blank map, and / or others. In other examples, the container type selection 202 is obtained automatically, such as by detecting or sensing physical characteristics / aspects and / or scannable elements of the sample container when the sample container is placed on or within the container holder 116.

[0034] 2 by the dashed arrow extending from the container type selection 202 to the container map 204. The container map 204 visually represents one or more characteristics of a sample container (e.g., a sample container positioned on or in a container holder 116 of the moveable stage 118) selected in accordance with the container type selection 202. Multiple container maps may be stored in the storage 104 for access in response to the container type selection 202.

[0035] 2, the vessel map 204 shows a number of wells 214. The number, size, and arrangement of wells 214 (or other features) shown on the vessel map 204 may depend on the vessel type selection 202. For example, the vessel map 204 of FIG. 2 includes 96 wells 214 and may have been selected for display within the graphical user interface 200 based on the vessel type selection 202 indicating that a 96-well sample vessel is positioned in the vessel holder 116 of the moveable stage 118.

[0036] As discussed above, the observation position marker 212 may be displayed in conjunction with the container map 204 to indicate the observation position of one or more observation or imaging optics of the sample analyzer 100 relative to a sample container positioned on or within the sample analyzer 100. Figure 2 conceptually illustrates the first position encoder 124 and the second position encoder 126, which correspond to the first position encoder 124 and the second position encoder 126 described above with reference to Figure 1. Figure 2 also illustrates first stage position data 206 acquired by the first position encoder 124 and second stage position data 208 acquired by the second position encoder 126. The format of the first and second stage position data 206 and 208 may take any suitable form, such as quadrature outputs.

[0037] The first stage position data 206 and the second stage position data 208 include or are based on sensor data acquired by the first position encoder 124 and the second position encoder 126, respectively. In this regard, as described above, the first stage position data 206 and the second stage position data 208 may indicate a position or a change in position of the moveable stage 118 (and thus a sample container positioned on or within the container holder 116 of the moveable stage 118). For example, the first stage position data 206 may indicate an absolute position or translation distance along a first dimension (e.g., the x dimension) and the second stage position data 208 may indicate an absolute position or translation distance along a second dimension (e.g., the y dimension). Where the data indicates a translation distance, the translation distance may be used in combination with a starting reference position (e.g., following a calibration step) to determine the stage and sample container positions.

[0038] Based on the position of the moveable stage 118 (and thus the sample container positioned in the container holder 116 of the moveable stage 118) as indicated by the first stage position data 206 and the second stage position data 208, an observation position 210 of the sample analyzer 100 can be determined (indicated in FIG. 2 by the dashed arrows extending from the first stage position data 206 and the second stage position data 208 to the observation position 210). The observation position 210 may include the positioning of one or more observation or imaging optics (e.g., objective lens 128) of the sample analyzer 100 relative to a sample container associated with the sample analyzer 100.

[0039] For example, as described above with reference to FIG. 1, the objective lens 128 may be fixed at a known position on the sample analyzer 100 when the objective lens 128 is prepared for imaging (e.g., when a particular objective lens 128 is selected via the objective lens selection wheel 134). Information regarding the known position of the objective lens 128 may be used to determine the positioning of the moveable stage 118 and its sample container relative to the objective lens 128. For example, if the first stage position data 206 and the second stage position data 208 indicate a translation distance per dimension, an offset may be determined between a reference position for calibration of the moveable stage 118 and the known position of the objective lens 128 on the sample analyzer 100. This offset may be used in combination with the received translation distance per dimension to determine an updated relative positioning between the objective lens 128 and a sample holder positioned on the moveable stage 118. If the first stage position data 206 and the second stage position data 208 indicate absolute positions, the absolute position data can be used in combination with the known position of the objective lens 128 to determine an updated relative positioning between the objective lens 128 and a sample holder positioned on the movable stage 118.

[0040] The observation position 210 may be used to generate an observation position marker 212 (illustrated in FIG. 2 by a dashed arrow extending from the observation position 210 to the observation position marker 212). As shown in FIG. 2, the observation position marker 212 may be displayed on the graphical user interface 200 (e.g., on the display 138) to communicate the observation position 210 of one or more observation or imaging optics (e.g., the objective lens 128) relative to a portion of a sample container as represented by the container map 204. For example, the graphical user interface 200 shows a container map 204 with the observation position marker 212 overlaid on the container map 204, thereby communicating the position of the objective lens 128 relative to a well 214 of the sample container represented by the container map 204. In this manner, a user can easily ascertain which well 214 the objective lens 128 is positioned to image. In the case of a sample container that does not include a well, such functionality may assist a user to easily ascertain which portion of the sample container is currently being imaged by the objective lens 128.

[0041] As the positions of the sample container and movable stage 118 are updated relative to the objective lens 128 (e.g., by manipulation of the x-adjustment knob 120 and / or the y-adjustment knob 122), updated first stage position data 206 (first dimension) and / or updated second stage position data 208 (second dimension) may be obtained (e.g., based on the output of the first position encoder 124 and / or the second position encoder 126). The updated first and second stage position data 206 and 208 may be used to generate an updated observation position 210. Thus, the positioning of the observation position marker 212 may be updated in real time based on the updated observation position 210, thereby providing a user with an intuitive tool for ascertaining an observation position associated with the sample analyzer 100.

[0042] In light of this disclosure, it will be appreciated that the particular form of the viewing location marker 212 shown in FIG. 2 is not a limitation of this disclosure, and that the viewing location marker 212 may take any suitable form.

[0043] 3 shows an exemplary graphical user interface 200 from FIG. 2. In addition to the vessel map 204, wells 214, and observation position markers 212, FIG. 3 shows a well identifier 302 (well ID 302). The well ID 302 may be determined based on the observation position 210 of one or more observation or imaging optics (e.g., objective lens 128) described above. For example, the location of a particular well 214 on a sample vessel may be predefined. Thus, the observation position 210 of the objective lens 128 relative to the sample vessel can be used to determine the positioning of the objective lens 128 relative to the known location of the particular well 214 of the sample vessel.

[0044] Each well of a particular sample container configuration may be pre-assigned a particular identifier value (e.g., an identifier having two elements, one indicating x-dimensional positioning and the other indicating y-dimensional positioning). If the observation position 210 of the objective lens 128 corresponds to a known position of a particular one of the wells 214 of the sample container (e.g., if the observation position 210 overlaps with at least a portion of the particular well or if the observation position 210 is within a threshold proximity to the particular well), the identifier value for the particular well may be displayed as a well ID 302.

[0045] 3, the observation location 210 (indicated by the observation location marker 212) is within the region defined by a particular well having an assigned well identifier "E7" (indicating that the well is in the fifth row (indicated by the "E" in "E7") of the seventh column (indicated by the "7" in "E7"). Thus, the well ID 302 displayed in the graphical user interface 200 is "E7." Such functionality may allow a user to easily identify which sample well the objective lens 128 of the sample analyzer 100 is positioned to image, which may assist the user in making and / or recording observations and associating them with particular portions of a sample container.

[0046] 3 illustrates that in some implementations, an image capture 304 operation may be performed by the sample analyzer 100 to save an image file 306 that depicts one or more samples in a sample container on the movable stage 118. In some examples, when image capture 304 is performed, a well ID 302 indicates a particular well of a sample container that is aligned with the observation position 210 of the objective lens 128 during image capture 304. Thus, in some implementations, the well ID 302 is automatically embedded in the image file 306 (as illustrated in FIG. 3 by the dashed line extending from the well ID 302 to the image file 306). The well ID 302 may be embedded in the image file 306 in a variety of ways, such as by adding the well ID 302 to the filename of the image file 306, by overlaying or adding image data representing the well ID 302 to a portion of the image file 306, by adding the well ID 302 to the metadata of the image file 306, and / or otherwise. Such functionality may allow a user to easily ascertain which sample well of a particular sample container is represented by the image file 306 when subsequently reviewing the image file 306 after a sample analysis session. In some examples, additional or alternative information is embedded in the image file 306, such as an x-position, y-position, and / or z-position associated with the observation position 210 (e.g., focus position and / or configuration).

[0047] FIG. 4 shows a conceptual diagram of saving a viewing position according to an implementation of the present disclosure. FIG. 4 shows the graphical user interface 200 of FIGS. 2 and 3. In addition to the container map 204 and the viewing position marker 212 based on the viewing position 210 described above, FIG. 4 shows that the graphical user interface 200 includes a viewing position save control 402. The viewing position save control 402 of FIG. 4 is shown as a selectable button on the graphical user interface 200. For example, a user can provide an input at an input device (e.g., a computer mouse, a touch screen, etc.) directed to the viewing position save control 402 to trigger a viewing position save operation. In view of the present disclosure, it will be understood that the viewing position save operation can be triggered in other ways within the scope of the present disclosure. For example, the viewing position save operation may additionally or instead be triggerable in response to a keystroke input, a button input, a gesture input, a voice input, and / or other means. The principles described herein in connection with saving a viewing position may be applied even when a viewing position save operation is triggered.

[0048] A save observation position operation may be triggered while one or more viewing or imaging optics (e.g., objective lens 128) of the sample analyzer 100 are positioned according to a viewing position 210 relative to a sample container positioned in the container holder 116 of the movable stage 118. In response to triggering the save observation position operation (e.g., by activation of a save observation position control 402), the viewing position 210 may be saved or added as a viewing position entry in the viewing position data structure 406, as shown in FIG. 4 by the dashed arrow extending from the viewing position 210 to the viewing position entry 410 in the viewing position data structure 406. The viewing position data structure 406 may comprise any number of entries, as indicated by the multiple viewing position entries 408 and 410 and ellipsis 412 depicted in FIG. 4. The viewing position data structure 406 may take any suitable data format and may be stored in any suitable manner (e.g., on the storage 104 of the sample analyzer 100 and / or on the storage of one or more remote systems). An observation position entry stored in the observation position data structure 406 may include an x-position, a y-position, a z-position, and / or other imaging / observation settings associated with the observation position for which the observation position entry is created.

[0049] Different viewing location entries in the viewing location data structure 406 may be assigned different names to allow a user to later distinguish between different saved viewing locations. For example, FIG. 4 illustrates an entry space for viewing location name 404, where a user may enter a name for a saved viewing location entry in the viewing location data structure 406 (e.g., as indicated in FIG. 4 by the dashed line extending from the viewing location name 404 to the viewing location entry 410 in the viewing location data structure 406). The text entered into the entry space for viewing location name 404 may be automatically associated with the saved viewing location upon invocation of a save viewing location operation (e.g., selection of the save viewing location control 402). In some examples, a default name is automatically entered into the entry space for viewing location name 404. The default name may be based, for example, on an ordering of the saved viewing location entries (e.g., "Pin 1" for the first saved viewing location entry, "Pin 2" for the second saved viewing location entry, etc.).

[0050] In some implementations, the observation locations data structure 406 (or one or more representations thereof) is accessible to allow a user to revisit saved observation locations represented in the observation locations data structure 406. In some examples, a representation of an observation location entry in the observation locations data structure 406 is automatically displayed (e.g., on the display 138 in combination with the graphical user interface 200) upon saving of the observation location entry.

[0051] In some examples, the observation location data structure is accessed by entering or selecting a control that facilitates access to it. For example, the example graphical user interface 200 of FIG. 4 includes a zoom control 414 that can be selected to trigger the display of a zoomed representation of the container map in combination with a representation of the observation location data structure 406.

[0052] FIG. 5 illustrates an exemplary graphical user interface 500 that provides a vessel map 502 that includes a zoomed or alternative representation of the vessel map 204 previously described with reference to FIGS. 2-4. In some examples, the vessel map 502 includes additional details or features as compared to the vessel map 204 described above. For example, as shown in FIG. 5, the vessel map 502 includes well row identifiers (e.g., "A," "B," "C," etc.) and well column identifiers (e.g., "1," "2," "3," etc.) to facilitate user navigation among and / or analysis of the various wells of the sample vessels represented by the vessel map 502. The exemplary graphical user interface 500 of FIG. 5 also illustrates an observation location marker 504 that includes guides extending outwardly from the observation location marker 504 in the x and y dimensions. The guides may assist a user in easily identifying the location of the observation location marker 504 relative to the array of wells of the sample vessels represented by the vessel map 502.

[0053] The graphical user interface of Figure 5 also illustrates viewing location entries 506 and viewing location entry markers 508. The viewing location entries 506 in Figure 5 are illustrated as an array of list entries, with the entries including names such as "pin 1", "pin 2", "pin 3", etc., which correspond to different viewing location entries that have been saved or added to the viewing location data structure 406 via a save viewing location operation (e.g., viewing location entries 408, 410 saved in the viewing location data structure 406 by operation of the save viewing location control 402, as described with reference to Figure 4).

[0054] The observation location entry markers 508 in FIG. 5 correspond to the observation location entries 506. Each observation location entry marker 508 is associated with and represents a respective observation location entry 506. The observation location entry markers 508 are shown as pins overlaid on the container map 502. The observation location entry markers 508 indicate the positioning of the observation location of each observation location entry 506 relative to the sample container represented by the container map 502. By presenting the observation location entries 506 and / or the observation location entry markers 508, embodiments of the present disclosure may easily communicate to a user the quantity, names, and positioning of the observation locations stored in the observation location data structure. For example, by viewing the observation location entries 506 in FIG. 5, a user may easily see that six observation locations are stored for the sample container represented by the container map 502. 5, a user can easily see that one or more observation location entries are stored in well B5, well C6, well C9 (3 entries), and well D8. From the above, a user can gain an understanding that multiple features / structures of interest are present in well C9, for example.

[0055] In some implementations, the observation location entries 506 and / or the observation location entry markers 508 are selectable to facilitate guided navigation to the saved observation locations. For example, the entries in the observation location entries 506 can include selectable list entries, and a user can direct user input to a particular list entry to initiate guided navigation to the observation location represented by the particular list entry. Similarly, for example, the observation location entry markers 508 can include selectable pins, and a user can direct user input to a particular pin to initiate guided navigation to the observation location associated with the particular pin.

[0056] 5 illustrates an example in which a particular list entry "pin 3" of the view location entry 506 is highlighted or emphasized. A corresponding particular selectable pin of the view location entry marker 508 is also highlighted or emphasized in well C6 of the container map 502. In some implementations, the particular list entry and / or the particular selectable pin may be highlighted as shown in FIG. 5 in response to a user selection of the particular list entry or the particular selectable pin.

[0057] In some examples, in response to the selection of a particular selectable pin and / or a particular list entry, a guided navigation is initiated toward the viewing position associated with the particular selectable pin and / or particular list entry (e.g., to a desired viewing position stored as a viewing position entry in a viewing position data structure, as described with reference to FIG. 4). For example, FIG. 5 illustrates a guide coordinate 510 that may be configured to guide the navigation of the movable stage 118 to align one or more viewing or imaging optics of the sample analyzer 100 with the viewing position associated with the particular selectable pin and / or particular list entry. As shown in FIG. 5, the guide coordinate 510 includes a ΔX coordinate and a ΔY coordinate. The ΔX coordinate may correspond to a first dimensional (x dimension) guide coordinate, and the ΔY coordinate may correspond to a second dimensional (y dimension) guide coordinate. For example, in some examples, the ΔX coordinate conveys the difference between the current x-dimension position of the observation position marker 504 relative to the container map 502 (or the current x-dimension position of the objective lens 128 relative to the sample container) and the target x-dimension position of the target observation position associated with the particular selectable pin and / or particular list entry (i.e., “pin 3”). Similarly, in some examples, the ΔY coordinate conveys the difference between the current y-dimension position of the observation position marker 504 relative to the container map 502 (or the current y-dimension position of the objective lens 128 relative to the sample container) and the target y-dimension position of the target observation position associated with the particular selectable pin and / or particular list entry (i.e., “pin 3”). The guide coordinate 510 may be updated based on the updated positioning of the observation position marker 504 (and the corresponding observation position of the objective lens 128) as the position of the moveable stage 118 is changed. In the illustrated example, when the ΔX guide coordinate reaches “0”, the x-dimension position of the observation position marker 504 corresponds to the target x-dimension position associated with “pin 3”. Similarly, when the ΔY guide coordinate reaches "0", the y dimension position of the view position marker 504 corresponds to the target y dimension position associated with "pin 3". In both cases, when the ΔX guide coordinate and the ΔY guide coordinate reach "0", the position of the view position marker 504 corresponds to the target view position associated with "pin 3".In some examples, in response to the observation position marker 504 reaching the target observation position, an additional or alternative user interface presentation (e.g., a change in color of the observation position marker 504, an audible sound, the display of an icon, etc.) is provided.

[0058] Thus, a user wishing to revisit the observation location associated with "pin 3" may select the list entry corresponding to "pin 3" or may select the selectable pin corresponding to "pin 3". Selection may cause guide coordinates 510 to display the difference in the x and y dimensions between the current position of observation location marker 504 and the target observation location associated with "pin 3". The user may then use guide coordinates 510 to modify the positioning of moveable stage 118 (and thus the sample container positioned thereon) to align observation location marker 504 with the target location associated with "pin 3" by causing the ΔX and ΔY guide coordinates to reach "0".

[0059] As discussed above, the observation position entry can include information such as a z position indicative of the focus position / configuration in addition to the x and y positions. Thus, in some examples, the guide coordinates 510 can include a ΔZ guide coordinate that allows the user to adjust the focus of the sample analyzer to match a pre-stored focus configuration.

[0060] In some examples, the observation location may include a graphical representation of a sample contained in a sample container. The sample in the sample container may include living cells. As a non-limiting example, the data may include a capture of the sample in the form of an image. The image may be associated with an observation location marker 504 for a particular list entry of the observation location entries 506. The use of images above is meant to be representative examples of possible graphical representations.

[0061] In some examples, as described above, the movable stage may be configured to operate in an automated manner, such as by operating motorized stage adjusters according to electronic adjustment instructions. Thus, in some implementations, re-navigation to a target viewing position associated with a saved viewing position entry in the viewing position data structure may be performed automatically in response to selection of a representation of the saved viewing position entry (e.g., a selectable pin, a selectable list element, etc.).

[0062] The foregoing examples have focused, at least in some respects, on implementations where the objective lens 128 remains at a stationary position in the xy dimensions on the sample analyzer during an imaging session, while the movable stage 118 is adjustable in the xy dimensions. However, the principles disclosed herein may be applied so long as the objective lens 128 and stage 118 are movable relative to one another. For example, the principles discussed herein in relation to tracking, storing, and / or revisiting observation positions may be applicable when the objective lens is adjustable / movable in the xy dimensions and the stage or sample container remains stationary in the xy dimensions on the sample analyzer 100 during an imaging session.

[0063] 6 illustrates an example graphical user interface 600 in which a zoomed representation of a container map 610 is provided in combination with a non-zoomed representation of a container map 602. The zoomed representation of the container map 602 is also associated with an observation location marker 604, an observation location entry marker 608, and an observation location entry 606, which may correspond to similarly named elements previously described. The container map 610 may likewise include corresponding observation location markers.

[0064] In some implementations, the vessel map 610 is displayed by default, but the zoomed representation of the vessel map 602 is only surfaced in response to selection of a zoom control (e.g., zoom control 414 shown in FIG. 4). FIG. 6 also illustrates that the vessel maps 610 and 602 may be displayed in combination with other microscopy controls and / or information displays. For example, the graphical user interface 600 of FIG. 6 shows illumination settings / controls, objective lens / phase ring information, focus information / controls, image capture controls, etc. In some examples, the zoomed vessel map 602 is overlaid on an image viewing window of the graphical user interface 600. In some examples, the zoomed vessel map 602 may be terminated in various ways, such as by reselecting the zoom control, selecting an explicit control to terminate the zoomed representation (e.g., an "X" icon as shown in the upper right corner of the vessel map shown in FIG. 6), and / or initiating another sample analysis operation (e.g., activating fluorescent or transmitted light illumination, and / or others). Such functionality can automatically expose / display relevant images based on user input (eg, activation of fluorescent or transmitted light illumination) while de-emphasizing the vessel map and / or presentation of view location markers.

[0065] The vessel maps 602 and 610 of Figure 6 represent different sample vessel well configurations as compared to the vessel maps shown and described with reference to Figures 2-5. For example, the vessel maps of Figures 2-5 include a 96 well configuration, while the vessel maps 602 and 610 of Figure 6 include a 384 well configuration. Figure 7 illustrates another exemplary graphical user interface 700 showing vessel maps 702 and 704 associated with a two-slide sample vessel configuration. In view of the above, the principles described herein may be applied to sample analysis of various types of sample vessels.

[0066] While the foregoing embodiments have focused, at least in some respects, on utilizing one or more encoders to obtain positioning information associated with the movable stage, the sample, and / or the objective lens, other hardware elements / techniques may be utilized to provide position information usable to facilitate dynamic presentation of a container map as discussed herein. As a non-limiting example, one or more image sensors may be utilized to capture the relative positioning of the objective lens with respect to the sample and / or the movable stage, and one or more image processing operations may be performed to determine a positioning information output based on the captured images. The positioning information output may be used to drive dynamically updated presentation of the container map and observation position markers.

[0067] Exemplary methods for tracking observation position during sample analysis The following description now refers to several methods and method operations that may be performed (e.g., utilizing one or more systems including components described herein, such as processor(s) 102, storage 104, I / O system(s) 110, communication system(s) 112, remote system(s) 114, other components of the sample analyzer 100, etc.). Although the operations of the methods are described in a particular order and shown in the flowcharts as occurring in a particular order, no particular order is required unless otherwise stated or because an operation is dependent upon another operation being completed before it can be performed. It should be understood that certain embodiments of the present disclosure may omit one or more of the operations described herein.

[0068] 8 illustrates an example flow chart 800 illustrating operations associated with tracking observation positions during sample analysis, according to an implementation of the present disclosure. The operations associated with flow chart 800 may incorporate and / or utilize one or more of the components described above with respect to Figures 1-7. Accordingly, some elements listed in the operations below include parenthetical references to elements described above for illustrative purposes.

[0069] Operation 802 of the flowchart 800 of FIG. 8 includes obtaining first and second stage position data, where the first stage position data indicates a first position of the movable stage in a first dimension and the second stage position data indicates a second position of the movable stage in a second dimension perpendicular to the first dimension. In some implementations, the first position data is obtained via a first position encoder configured to generate a first output indicative of the first position data of the movable stage in the first dimension. Similarly, in some implementations, the second position data is obtained via a second position encoder configured to generate a second output indicative of the second position data of the movable stage in the second dimension. Further, in some implementations, the first position encoder or the second position encoder comprises an incremental encoder, such that the first output or the second output indicates a translation distance.

[0070] In some examples, a first position of the movable stage in a first dimension and / or a second position of the movable stage in a second dimension can be determined based on a stage calibration, which can include translating the movable stage to a calibration reference position to measure a translation distance from the reference position to determine the position of the movable stage.

[0071] In some implementations, the first position encoder or the second position encoder comprise an absolute encoder, such that the first output or the second output indicates an absolute position.

[0072] The first or second position encoder can comprise a linear encoder, a rotary encoder (e.g., disposed on a rotatable adjustment knob for translating the moveable stage), etc. In some examples, the first or second position encoder comprises a magnetic encoder, an optical encoder, or a capacitive encoder.

[0073] Operation 804 of the flowchart 800 includes determining an observation position of one or more viewing or imaging optics relative to the moveable stage based on the first and second stage position data. The observation position may represent a relative positioning between one or more viewing or imaging optics of the sample analyzer and a sample container positioned on the moveable stage of the sample analyzer.

[0074] An operation 806 of the flow diagram 800 includes displaying a vessel map on the display, the vessel map including a visual representation of the sample vessel associated with the movable stage. In some examples, the vessel map is selected based on user input. The vessel map can show multiple sample wells associated with the sample vessel.

[0075] Operation 808 of flow diagram 800 includes displaying an observation position marker overlaid on the container map, the observation position marker indicating an observation position of one or more observation or imaging optics relative to the sample container represented by the container map. In some implementations, the display of the observation position marker relative to the container map is updated in response to obtaining updated first and / or updated second stage position data indicating an updated first position of the moveable stage in the first dimension and / or an updated second position of the moveable stage in the second dimension.

[0076] Operation 810 of the flowchart 800 includes identifying a particular sample well among a plurality of sample wells associated with the sample container, the particular sample well positionally corresponding to an observation location of one or more viewing or imaging optics relative to the sample container. Further, operation 812 of the flowchart 800 includes displaying a sample well identifier on a display, the sample well identifier identifying the particular sample well among the plurality of sample wells associated with the sample container. Further, operation 814 of the flowchart 800 includes automatically embedding the sample well identifier in an image file in response to detecting an image capture operation to capture an image at the observation location.

[0077] Operation 816 of flow diagram 800 includes, in response to activation of an observation position save control while one or more observation or imaging optics are positioned according to an observation position relative to the sample container, saving the observation position as an observation position entry in an observation position data structure that may be accessible to enable a user to revisit the saved observation positions represented in the observation position data structure.

[0078] Operation 818 of the flow diagram 800 includes displaying a representation of the observation location data structure including a representation of each observation location entry of the observation location data structure. In some implementations, the representation of the observation location data structure is displayed in response to activation of a zoom control. A display of the zoomed representation of the container map may be provided in combination with the representation of the observation location data structure. In some implementations, the display of the zoomed representation of the container map is automatically terminated in response to detecting activation of a fluorescent or transmitted light illumination control.

[0079] In some implementations, each representation of each view location entry in the view location data structure includes a selectable list entry. Additionally or alternatively, each representation of each view location entry in the view location data structure may comprise a selectable pin that is overlaid on the container map.

[0080] In some implementations, selecting a particular representation of a particular observation position entry of the observation position data structure displays guide coordinates configured to facilitate user navigation of the moveable stage relative to the one or more observation or imaging optics to align the one or more observation or imaging optics to the particular observation position associated with the particular observation position entry. The guide coordinates may include first dimension guide coordinates and second dimension guide coordinates. The first dimension guide coordinates may include a difference between a current first position of the one or more observation or imaging optics relative to the sample container and a desired first position of the one or more observation or imaging optics relative to the sample container in the first dimension. The second dimension guide coordinates may include a difference between a current second position of the one or more observation or imaging optics relative to the sample container and a desired second position of the one or more observation or imaging optics relative to the sample container in the second dimension. The desired first position and the desired second position may be obtained from the selected observation position entry of the observation position data structure.

[0081] Additional Computer System Details The disclosed embodiments may comprise or utilize special purpose or general purpose computers including computer hardware, as discussed in more detail below. The disclosed embodiments may also include physical media and other computer readable media for carrying or storing computer executable instructions and / or data structures. Such computer readable media may be any available media accessible by a general purpose or special purpose computer system. Computer readable media that store computer executable instructions in the form of data are one or more "physical computer storage media" or "hardware storage device(s)". Computer readable media that simply hold computer executable instructions without storing them are "transmission media". Thus, by way of example and not limitation, the present embodiments may comprise at least two distinctly different kinds of computer readable media: computer storage media and transmission media.

[0082] Computer storage media (also known as "hardware storage") includes RAM, ROM, EEPROM, CD-ROM, RAM-based solid state drives ("SSD"), flash memory, phase-change memory, and The term "hardware" refers to a computer-readable hardware storage device, such as a general-purpose or special-purpose computer-accessible memory, "PCM," or other type of memory, or other optical disk storage, magnetic disk storage, or other magnetic storage device, or any other medium that can be used to store desired program code means in the form of computer-executable instructions, data, or data structures in the hardware and that can be accessed by a general-purpose or special-purpose computer.

[0083] A "network" is defined as one or more data links that enable the transfer of electronic data between computer systems and / or modules and / or other electronic devices. When information is transferred or provided over a network or another communications connection (either hardwired, wireless, or a combination of hardwired or wireless) to a computer, the computer properly views the connection as a transmission medium. Transmission media can be used to carry program code in the form of computer-executable instructions or data structures and can include networks and / or data links accessible by a general-purpose or special-purpose computer. Combinations of the above are also included within the scope of computer-readable media.

[0084] Furthermore, upon reaching various computer system components, program code means in the form of computer executable instructions or data structures can be automatically transferred from a transmission computer readable medium to a physical computer storage medium (or vice versa). For example, computer executable instructions or data structures received over a network or data link may be buffered in a RAM in a network interface module (e.g., a "NIC") and eventually transferred to the computer system RAM and / or to a less volatile computer readable physical storage medium of the computer system. It should therefore be understood that computer readable physical storage media may be included in computer system components that also (or primarily) utilize a transmission medium.

[0085] Computer-executable instructions include, for example, instructions and data that cause a general purpose computer, special purpose computer, or special purpose processing device to perform a certain function or group of functions. Computer-executable instructions may be, for example, binaries, intermediate format instructions such as assembly language, or even source code.

[0086] The disclosed embodiments may include or utilize cloud computing. The cloud model may consist of a variety of characteristics (e.g., on-demand self-service, wide area network access, resource pooling, rapid elasticity, measured service, etc.), service models (e.g., Software as a Service ("SaaS"), Platform as a Service ("PaaS"), Infrastructure as a Service ("IaaS"), and deployment models (e.g., private cloud, community cloud, public cloud, hybrid cloud, etc.).

[0087] Those skilled in the art will appreciate that the present invention may be practiced in a network computing environment with many types of computer system configurations including personal computers, desktop computers, laptop computers, message processors, handheld devices, multiprocessor systems, microprocessor-based or programmable consumer electronics, network PCs, minicomputers, mainframe computers, mobile phones, PDAs, pagers, routers, switches, wearable devices, etc. The present invention may also be practiced in a distributed system environment where tasks are performed by multiple computer systems (e.g., local and remote computer systems) that are linked through a network (either by wired data links, wireless data links, or a combination of wired and wireless data links). In a distributed system environment, program modules may be located in local and / or remote memory storage devices.

[0088] Alternatively or additionally, the functions described herein may be performed, at least in part, by one or more hardware logic components. For example, without limitation, exemplary types of hardware logic components that may be used include Field-programmable Gate Arrays (FPGAs), Program-specific Integrated Circuits (ASICs), Application-specific Standard Products (ASSPs), System-on-a-chip systems (SOCs), Complex Programmable Logic Devices (CPLDs), central processing units (CPUs), graphics processing units (GPUs), and / or others.

[0089] As used herein, the terms "executable module," "executable component," "component," "module," or "engine" may refer to a hardware processing unit or a software object, routine, or method that may be executed on one or more computer systems. The different components, modules, engines, and services described herein may be implemented as objects or processors (e.g., as separate threads) executing on one or more computer systems.

[0090] In some embodiments, the systems of the present disclosure may comprise or be configurable to execute any combination of software and / or hardware components operable to facilitate processing using machine learning models or other artificial intelligence based structures / architectures. For example, the one or more processors may include or utilize hardware components and / or computer-executable instructions operable to execute functional blocks and / or processing layers configured in the form of, for example, a single layer neural network, a feedforward neural network, a radial basis function network, a deep feedforward network, a recurrent neural network, a long-short term memory (LSTM) network, a gated recurrent unit, an autoencoder neural network, a variational autoencoder, a denoising autoencoder, a sparse autoencoder, a Markov chain, a Hopfield neural network, a Boltzmann machine network, a restricted Boltzmann machine network, a deep belief network, a deep convolutional network (or convolutional neural network), a deconvolutional neural network, a deep convolutional inverse neural network, a generative adversarial network, a liquid state machine, an extreme learning machine, an echo state network, a deep residual network, a Kohonen network, a support vector machine, a neural Turing machine, or the like, as non-limiting examples.

[0091] Various modifications and / or alterations of the features of the invention exemplified herein, and additional applications of the principles set forth herein, which will occur to those skilled in the relevant art and in possession of this disclosure, may be made to the embodiments without departing from the spirit and scope of the invention as defined by the claims, and should be considered within the scope of this disclosure. Thus, while various aspects and embodiments have been disclosed herein, other aspects and embodiments are contemplated. Although many methods and components similar or equivalent to those described herein may be used to practice the embodiments of the disclosure, only specific components and methods are described herein.

[0092] It will also be understood that systems, devices, products, kits, methods, and / or processes according to certain embodiments of the present disclosure may include, incorporate, or otherwise include properties or features (e.g., components, members, elements, parts, and / or portions) described in other embodiments disclosed and / or described herein. Thus, various features of a particular embodiment may be compatible, combined, included, and / or incorporated with other embodiments of the present disclosure. Thus, the disclosure of a particular feature in relation to a particular embodiment of the present disclosure should not be construed as limiting the application or inclusion of that feature to the particular embodiment. Rather, it will be understood that other embodiments may include such features, members, elements, parts, and / or portions without necessarily departing from the scope of the present disclosure.

[0093] Moreover, unless a feature is described as requiring another feature in combination, any feature herein can be combined with any other feature of the same or different embodiments disclosed herein. Moreover, various well-known aspects of example systems, methods, devices, and the like have not been described in particular detail herein to avoid obscuring aspects of the example embodiments. However, such aspects are also contemplated herein.

[0094] The present disclosure may be embodied in other specific forms without departing from the spirit or essential characteristics of the present invention. The described embodiments are to be considered in all respects as illustrative and not restrictive. The scope of the present invention is therefore indicated by the appended claims rather than by the foregoing description. Although specific embodiments and details have been included in this specification and the accompanying disclosure for the purpose of illustrating embodiments of the present disclosure, it will be apparent to those skilled in the art that various modifications can be made in the methods, products, devices, and apparatuses disclosed herein without departing from the scope of the disclosure or the invention as defined by the appended claims. All changes that come within the meaning and range of equivalency of the claims are to be embraced within their scope.

Claims

1. 1. A sample analyzer having a movable stage, The movable stage is a sample vessel holder configured to receive a sample vessel; a stage position adjuster configured to translate the movable stage in at least a first dimension and a second dimension perpendicular to the first dimension; a first position encoder configured to generate a first output indicative of a first position of the movable stage in the first dimension; a second position encoder configured to generate a second output indicative of a second position of the movable stage in the second dimension. Sample analyzer.

2. The sample analyzer of claim 1 , wherein the sample vessel holder comprises a retaining member configured to retain the sample vessel in a final position within the sample vessel holder.

3. 10. The sample analyzer of claim 1, wherein the first position encoder or the second position encoder comprises an incremental encoder, and the first output or the second output indicates a translation distance.

4. 10. The sample analyzer of claim 1, wherein the first position encoder or the second position encoder comprises an absolute encoder, and the first output or the second output indicates an absolute position.

5. The sample analyzer of claim 1 , wherein the first position encoder or the second position encoder comprises a linear encoder.

6. The sample analyzer of claim 1 , wherein the first position encoder or the second position encoder comprises a magnetic encoder, an optical encoder, or a capacitive encoder.

7. The sample analyzer of claim 1 , wherein the first position encoder or the second position encoder comprises a rotary encoder.

8. The sample analyzer of claim 7 , wherein the rotary encoder is positioned on a rotatable adjustment knob configured to facilitate translation of the moveable stage.

9. The sample analyzer of claim 1 , wherein the first output and the second output comprise quadrature outputs.

10. A display and one or more processors; one or more hardware storage devices that store instructions executable by the one or more processors; 1. A sample analyzer comprising: By configuring the sample analyzer, obtaining first stage position data indicative of a first position of a movable stage in a first dimension and second stage position data indicative of a second position of the movable stage in a second dimension perpendicular to the first dimension; determining an observation position of one or more observation or imaging optics relative to the movable stage based on the first and second stage position data; displaying on the display a container map, the container map including a visual representation of a sample container associated with the movable stage; displaying an observation position marker overlaid on the container map, the observation position marker indicating the observation position of the one or more observation or imaging optics relative to the sample container represented by the container map; Sample analyzer.

11. 11. The sample analyzer of claim 10, wherein the instructions are executable by the one or more processors to further configure the sample analyzer to update a display of the observation position marker relative to the container map in response to obtaining updated first stage position data and / or updated second stage position data indicating an updated first position of the movable stage in the first dimension and / or an updated second position of the movable stage in the second dimension.

12. 11. The sample analyzer of claim 10, wherein the first position of the movable stage in the first dimension and / or the second position of the movable stage in the second dimension are determined based on a stage calibration, the stage calibration including translating the movable stage to a calibration reference position.

13. The sample analyzer of claim 10 , wherein the first position of the movable stage in the first dimension and / or the second position of the movable stage in the second dimension are determined based on absolute position measurements.

14. The sample analyzer of claim 10 , wherein the vessel map is selected based on user input.

15. The sample analyzer of claim 10 , wherein the container map indicates a number of sample wells associated with the sample container.

16. the instructions are executable by the one or more processors; identifying a particular sample well of the plurality of sample wells associated with the sample container, the particular sample well positionally corresponding to the observation location of the one or more observation or imaging optics relative to the sample container; further configuring the sample analyzer to display on the display a sample well identifier that identifies the particular sample well from the plurality of sample wells associated with the sample container.

16. The sample analyzer of claim 15.

17. the instructions are executable by the one or more processors; further configuring the sample analyzer to automatically embed the sample well identifier in an image file in response to detecting an image capture motion to capture an image at the viewing position.

17. The sample analyzer of claim 16.

18. the instructions are executable by the one or more processors; further configuring the sample analyzer to, in response to activation of an observation position save control while the one or more observation or imaging optics are positioned according to the observation position relative to the sample container, save the observation position as an observation position entry in an observation position data structure, the observation position data structure being accessible to enable a user to revisit the saved observation positions represented in the observation position data structure. The sample analyzer of claim 10.

19. the instructions are executable by the one or more processors; further configuring the sample analyzer to display a representation of the observation location data structure, the representation including a representation of each observation location entry of the observation location data structure.

20. The sample analyzer of claim 18.

20. 20. The sample analyzer of claim 19, wherein each representation of each view location entry in the view location data structure comprises a selectable list entry.

21. 20. The sample analyzer of claim 19, wherein each representation of each view location entry in the view location data structure includes a selectable pin overlaid on the vessel map.

22. 21. The sample analyzer of claim 20, wherein selecting a particular representation of a particular observation position entry in the observation position data structure displays guide coordinates configured to facilitate user navigation of the movable stage relative to the one or more observation or imaging optical systems to align the one or more observation or imaging optical systems to the particular observation position associated with the particular observation position entry.

23. 23. The sample analyzer of claim 22, wherein the guide coordinates include first dimension guide coordinates and second dimension guide coordinates, the first dimension guide coordinates including a difference between a current first position of the one or more observation or imaging optics relative to the sample vessel and a desired first position of the one or more observation or imaging optics relative to the sample vessel in the first dimension, and the second dimension guide coordinates including a difference between a current second position of the one or more observation or imaging optics relative to the sample vessel and a desired second position of the one or more observation or imaging optics relative to the sample vessel in the second dimension, and the desired first position and the desired second position are obtained from the selected observation position entry in the observation position data structure.

24. the instructions are executable by the one or more processors; configuring the sample analyzer to, in response to activation of a zoom control, (i) display a zoomed representation of the vessel map, and (ii) display the representation of the view location data structure.

20. The sample analyzer of claim 19.

25. the instructions are executable by the one or more processors; configuring the sample analyzer to automatically terminate display of the zoomed representation of the vessel map in response to detecting activation of a fluorescent or transmitted light illumination control.

25. The sample analyzer of claim 24.

Images