Systems and methods for counting cells

Abstract

To provide systems and methods for counting cells.SOLUTION: According to at least one aspect, a system configured to count cells in a vessel is provided. The system comprises an imaging system configured to image cells in the vessel, and a controller coupled to the imaging system. The controller is configured to control the imaging system to capture a focused image of the cells, and estimate the number of cells in the focused image. The controller is configured to control the imaging system to capture a focused image of the cells at least in part by controlling the imaging system to capture a plurality of images of the cells in a plurality of focal planes, determining an area of at least one cell in each of the images, and selecting one of the images as the focused image using the area of the at least one cell in the plurality of images.SELECTED DRAWING: None

Description

[Technical Field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit under 35 U.S.C. §119(e) of U.S. Provisional Application No. 62 / 508,953, entitled "SYSTEMS AND METHODS FOR COUNTING CELLS," filed May 19, 2017, which is incorporated herein by reference in its entirety.

[0002] Field Various aspects of the technology described herein relate to techniques for automatically counting cells in a container. Some aspects relate to the implementation of these techniques in automated cell counters and cell culture incubators. [Background technology]

[0003] background Some scientific experiments may require cell cultures with a minimum concentration (e.g., 1,300,000 cells per milliliter) and / or a minimum number (e.g., 10,000,000 cells per milliliter) of cells. For these experiments, a manual cell count is typically performed using a hemacytometer to confirm that the cell culture being used for the experiment contains a sufficient concentration and / or number of cells. The hemacytometer may have, for example, a chamber with grid lines forming a box of a predetermined size configured to receive a sample from the cell culture. An operator may view the hemacytometer under a microscope and count the number of cells in one or more boxes formed by the grid lines. The operator may thereby use the manually counted cell number in combination with the known size of the box to identify the cell concentration in the sample. The total number of cells in the sample may be identified by multiplying the identified cell concentration by the size (e.g., volume) of the sample. Summary of the Invention [Means for solving the problem]

[0004] Abstract According to at least one aspect, a system is provided that includes an imaging system configured to image a plurality of cells in a container at multiple focal planes, and at least one controller coupled to the imaging system. The at least one controller is coupled to a memory that includes instructions that, when executed, control the imaging system to capture multiple images of at least some of the cells, where each of the multiple images is captured in a distinct focal plane of the multiple focal planes; determine an area of ​​at least one cell from at least some of the cells in each of the multiple images; select an image from the multiple images as a focused image using the area of ​​the at least one cell in at least some of the multiple images; and estimate the number of cells in the focused image.

[0005] According to at least one aspect, a method is provided that includes receiving a plurality of cells in a container, capturing focused images of at least some cells within the plurality of cells, and estimating, using at least one controller, a number of cells within the focused images. Capturing the focused images of at least some cells within the plurality of cells includes capturing, using an imaging system, a plurality of images of the at least some cells, each of the plurality of images being captured within a distinct focal plane of a plurality of focal planes; determining, using the at least one controller, an area of ​​at least one cell from the at least some cells in each of the plurality of images; and selecting, using the at least one controller, an image from the plurality of images as the focused image using the area of ​​the at least one cell in at least some of the plurality of images.

[0006] According to at least one aspect, an automated cell counter is provided, the automated cell counter including: a container mount configured to receive a container containing a plurality of cells; an imaging system configured to image the plurality of cells in a plurality of focal planes; and at least one controller coupled to the imaging system. The at least one controller is coupled to a memory containing instructions that, when executed, control the imaging system to capture a plurality of images of at least some of the cells, each of the plurality of images being captured in a distinct focal plane of the plurality of focal planes; determine an area of ​​at least one cell from at least some of the cells in each of the plurality of images; select an image from the plurality of images as a focused image using the area of ​​the at least one cell in at least some of the plurality of images; and estimate the number of cells in the focused image.

[0007] According to at least one aspect, a system is provided that includes an imaging system configured to image a plurality of cells in a container, and at least one controller coupled to the imaging system. The at least one controller is coupled to a memory that includes instructions that, when executed, control the imaging system to capture a plurality of focused images of at least some cells in the plurality of cells, and determine a number of cells in the focused images, at least in part, by identifying a plurality of objects in the focused images, classifying a subset of the plurality of objects as cells, and counting the number of cells in the subset of the plurality of objects classified as cells.

[0008] According to at least one aspect, a cell culture incubator is provided, the cell culture incubator including an incubator cabinet configured to receive a container for storing a plurality of cells, an imaging system configured to image the plurality of cells, and at least one controller coupled to the imaging system. The at least one controller is coupled to a memory containing instructions that, when executed, control the imaging system to capture a plurality of images of at least some of the cells, where each of the plurality of images is captured within a distinct focal plane of a plurality of focal planes; determine an area of ​​at least one cell from at least some of the cells in each of the plurality of images; select an image from the plurality of images as a focused image using the area of ​​the at least one cell in at least some of the plurality of images; and estimate the number of cells in the focused image. [Brief explanation of the drawings]

[0009] Various aspects and embodiments are described with reference to the following figures. It should be understood that the figures are not necessarily drawn to scale. Items that appear in more than one figure are designated by the same or similar reference numerals in all figures in which they appear.

[0010] [Figure 1A] FIG. 1A is a diagram illustrating a top view of a vessel containing cells, according to some embodiments of the technology described herein.

[0011] [Figure 1B] FIG. 1B is a diagram illustrating a cross-sectional view of a vessel containing cells, according to some embodiments of the technology described herein.

[0012] [Figure 2] FIG. 2 is a diagram illustrating an exemplary process for counting cells in an image, according to some embodiments of the techniques described herein.

[0013] [Figure 3]FIG. 3 is a flowchart of an exemplary process for counting cells in a container, according to some embodiments of the technology described herein.

[0014] [Figure 4] FIG. 4 is a schematic diagram of an exemplary cell culture incubator, according to some embodiments of the technology described herein.

[0015] [Figure 5] FIG. 5 is a schematic diagram of an exemplary automated cell counter according to some embodiments of the technology described herein.

[0016] [Figure 6] 6A and 6B are diagrams illustrating an example imaging system in accordance with some embodiments of the techniques described herein.

[0017] [Figure 7] FIG. 7 is a diagram of an example controller in accordance with some embodiments of the techniques described herein. DETAILED DESCRIPTION OF THE INVENTION

[0018] Detailed Description As discussed above, the cell concentration and / or cell number of cells in a cell culture may need to be identified for an experiment. Traditionally, an operator may count the number of cells in a cell culture by taking a representative sample from the culture and counting the number of cells in the sample. Given the small size of individual cells, an operator typically places the sample in a container (such as a hemocytometer) and views the container (including the cells) under a microscope. However, the operator will typically observe foreign matter, such as air bubbles and / or debris, in the sample. Thus, the operator must typically visually distinguish between the cells and foreign matter in the sample. An exemplary view of a sample in a container as viewed by an operator is shown in FIG. 1A. As shown, the view includes live cells 104, air bubbles 106, dead cells 108, and debris 110 on the surface of the container 102. Furthermore, the operator must typically focus the microscope on the live cells 104 to obtain such a view of the sample as shown in FIG. 1A. Given the small size of the live cells 104, an operator may not be able to see the live cells 104 if the microscope is out of focus by 10 microns. Figure 1B shows a cross-sectional view of a container 102 containing a sample and a set of exemplary focal planes 112 that may be selected by the operator. As shown, the majority of focal planes within the set of focal planes 112 do not intersect with the live cells 104.

[0019] The inventors have recognized that manually counting cells in a vessel (such as a hemocytometer) is typically a time-consuming process that requires the judgment of a laboratory technician and is subject to human error. For example, a human may select an incorrect focal plane, where certain types of debris appear similar to live cells and include the debris in the total cell count. Furthermore, undercounting and / or overcounting the number of cells in a cell culture can lead scientists to use an inappropriate cell culture throughout an experiment, which can result in a failed experiment. Thus, aspects of the present disclosure relate to techniques for automatically counting cells in a vessel. For example, the resulting cell counts produced by use of these techniques may produce counts that deviate from manual counts by only ±5%. These techniques improve over traditional cell counting techniques by providing a rapid and accurate method for counting cells (e.g., cells in a cell culture), which reduces human error and facilitates the completion of successful experiments.

[0020] The present inventors understand that analyzing images of cells captured in an inaccurate focal plane (e.g., a plane in which the cells are not in focus) can adversely affect the accuracy of the resulting cell count. Therefore, the present inventors have devised a new technique for identifying a focal plane (or even a focal distance) so that the cells are in focus. The present inventors understand that the area of ​​the cells can vary based on the focal plane selected. For example, the edges of the cells may appear blurred in the focal plane when the cells are not in focus, thereby making the cells appear larger. Conversely, the edges of the cells may appear sharp in the focal plane in which the cells are in focus, thereby making the cells appear smaller. Thus, the focal plane in which the cells are in focus may be the focal plane in which the area of ​​the cells is smallest.

[0021] Once a suitable focal plane is identified, one or more image processing techniques devised by the present inventors can be employed to estimate the number of cells in the focused image. For example, one or more objects can be identified in the focused image. These objects can be, for example, continuous regions of pixels in the foreground of the image. Once the objects are identified, one or more features can be identified for one or more of the objects, such as size and / or shape, and used to classify the objects. For example, the objects can be classified as live cells, dead cells, or debris based on one or more features of the objects. Once the objects are classified, the number of objects classified as cells (e.g., live cells or dead cells) can be counted to estimate the total number of cells in the focused image.

[0022] Some aspects of the technology described herein relate to a system (such as an automated cell counter or a cell culture incubator) configured to automatically count cells in a container. The container may be configured to receive cells in a fluid. Exemplary containers include flasks, bottles, bags, and plates. The system may include an imaging system configured to image a plurality of cells in the container in multiple focal planes. The imaging system may be implemented, for example, as a microscope (e.g., a bright-field microscope). The imaging system may include an imaging unit configured to detect light and one or more optical elements (e.g., lenses, mirrors, optical filters, and light sources) for changing the properties of the light.

[0023] The system may include a controller coupled (e.g., communicatively coupled) to the imaging system. The controller may be implemented, for example, using a processor coupled to a memory and / or non-volatile storage device. The controller may be configured to control the imaging system to capture focused images (e.g., focused bright-field images) of a plurality of cells using the imaging system. For example, the controller may send instructions to the imaging system to trigger the imaging system to capture multiple images in different focal planes (or even focal lengths). Such a plurality of images may be referred to as a "Z-stack" because it may include two-dimensional (x / y) images at different focal lengths (different "z" coordinates) for an imaging device (e.g., a camera) in the imaging system. The controller may then analyze the multiple images captured in the different focal planes and identify an image within the plurality of images that is a focused image. In some embodiments, the identified image may be referred to as a focused image because the image is identified from the plurality of images based on a quantitative estimate of the degree to which the image may be "focused." For example, an image within the plurality of images that is a focused image may have the smallest area of ​​cells. Thereby, the focused image may be selected, for example, by determining the area of ​​at least one cell in each of the multiple images and selecting one image from the multiple images as the focused image with the cell with the smallest area.

[0024] Once the focused image is identified, the controller may be configured to estimate the number of cells (e.g., live cells, dead cells, or a combination thereof) in the focused image. For example, the controller may be configured to identify multiple objects in the focused image and classify the objects in the focused image as, for example, a single live cell, a live cell clump, a dead cell, or debris. Once the objects are classified, the number of live cells (e.g., viable cells) may be estimated by counting the number of objects classified as live cells (e.g., a single live cell and a live cell clump). Similarly, the number of dead cells may also be identified by counting the number of objects classified as dead cells. Furthermore, the total number of cells may be identified by combining the number of dead cells and the number of live cells. The controller may be configured to classify the objects in any of a variety of ways. For example, the controller may classify the objects by identifying one or more features of the objects and providing the one or more features as input to a classifier. The classifier may be configured (e.g., trained) to provide an indication of the class to which the object belongs based on the input features. Exemplary classifiers that may be employed include decision trees, neural networks, discriminant functions, Bayesian networks, and support vector machines.

[0025] It should be understood that the embodiments described herein can be implemented in any of numerous ways. Examples of specific implementations are provided below for illustrative purposes only. It should be understood that these embodiments and provided features / capabilities can be used individually, all together, or in any combination of two or more, as aspects of the technology described herein are not limited in this respect.

[0026] As discussed above, the number of cells in a container can be counted by capturing focused images of the cells in the container and analyzing the focused images using automated image processing techniques. Figure 2 is a schematic diagram illustrating an exemplary process 200 that can be implemented to estimate the number of cells in a container. Process 200 can be implemented by any of a variety of systems, including, for example, a cell culture incubator (e.g., cell culture incubator 400) or an automated cell counter (e.g., automated cell counter 500). As shown, multiple images 201 of the cells in the container in different focal planes can be captured. A focused image 202 can then be selected from the multiple images 201, and the foreground 206 of the focused image 202 can be separated from the background 204 of the focused image 204, such that the foreground 206 includes a portion of the image that includes cells and the background 204 includes a portion of the image that does not include cells. Once the foreground 206 is separated from the background 204, an object 208 can be identified in the focused image 202 (e.g., in the foreground 206) that can be classified (e.g., classified as a living cell mass 210). Once the object 208 is classified, the number of cells in the object 208 can be counted.

[0027] The multiple images 201 may be captured in multiple different focal planes (e.g., the multiple images 201 may be a Z-stack). The focal planes may be uniformly spaced (e.g., the focal planes are separated by 2 microns) or non-uniformly spaced (e.g., some focal planes are separated by 1 micron, while others are separated by 3 microns). The multiple images 201 may be, for example, bright-field images captured by an imaging system such as imagers 600A or 600B shown in FIGS. 6A and 6B, respectively.

[0028] The focused image 202 may be selected from the plurality of images 201 by analyzing the area of ​​cells in each of the plurality of images. For example, the area of ​​a cell may be smallest in the focused image and smaller in the remaining images. The focused image may thereby be selected from the plurality of images by selecting the image with the smallest area of ​​the cell (or conversely, the largest non-cellular area). The area of ​​a cell in an image may be identified in any of a variety of ways. In some embodiments, the area of ​​a cell may be identified for each image in the plurality of images 201 by (1) separating the background 204 from the foreground 206, (2) identifying objects in the foreground 206 that are within a certain dimension (e.g., the typical dimension of a single cell), and (3) summing the areas of the objects.

[0029] The background 204 may be segmented from the foreground 206 in the focused image using edge detection techniques, such as applying one or more thresholds to the focused image 202. The thresholds may separate pixels based on their intensity values. For example, pixels having intensity values ​​below the threshold may be classified as the foreground 206, and pixels having intensity values ​​above the threshold may be classified as the background 204. Any of a variety of methods may be employed to identify a particular threshold to use, as would be understood by one skilled in the art. For example, the threshold may be identified using the Otsu thresholding method. It should be understood that more than one threshold may be employed to separate the foreground 206 from the background 204. For example, the image may be subdivided into multiple segments, and a separate threshold may be identified for each of the multiple segments to separate the background 204 from the foreground 206. In some embodiments, the result of the segmentation of the background 204 from the foreground 206 may be represented by a mask, such as a binary mask, that indicates, for each pixel in the image, whether the pixel belongs to the foreground 206 or the background 204.

[0030] In some embodiments, after thresholding the image and completing the mask, one or more actions may be performed. For example, a thresholding operation may have classified the centers of live cells as background 204 due to their light color. Only the outer edges of the live cells may then be classified as part of the foreground 206. In this example, holes in the middle of areas within foreground 206 may be added to the mask (e.g., reclassified as foreground). Additionally (or alternatively), artifacts initially detected as part of foreground 206 may be moved to background 204 and / or removed entirely from focused image 202. For example, a group of pixels in foreground 206 with fewer than a threshold number of pixels (e.g., 5 pixels, 10 pixels, etc.) may be likely to be artifacts and may be moved to background 204. In another example, a smoothing filter that reduces intensity variations between pixels may be applied to focused image 202 (or just foreground 206). Large intensity variations between two adjacent pixels are likely caused by noise and may be reduced thereby.

[0031] The object 208 may be identified in the focused image 206, for example, by identifying a contiguous region of pixels in the foreground 204 (e.g., as indicated by a mask) as the object. Once the object 208 is identified, the object 208 may be classified, for example, by identifying one or more features of the object 208 and providing the identified features of the object 208 as inputs to a classifier. Exemplary features of the object 208 that may be identified include morphological features, light intensity features, and texture features. Morphological features may, for example, relate to the size and / or shape of the object 208. Light intensity features may, for example, relate to characteristics of pixel intensity values ​​that detract from the object 208. Texture features may, for example, relate to the appearance of the surface and / or cross-section of the object 208. Once the features of the object 208 are identified, these features may be used as inputs to a classifier configured (e.g., trained) to distinguish between different classes of objects. Exemplary classifiers that may be employed include decision trees, neural networks, discriminant functions, Bayesian networks, and support vector machines. The output of the classifier may be an indication of the class to which the object 208 belongs. For example, the output of the classifier may indicate whether the object 208 is a single live cell, a cell clump, a dead cell, or an artifact. It should be understood that the particular set of classes that the classifier may be configured to distinguish may vary based on the particular implementation.

[0032] The result 212 may be generated, for example, by counting the number of objects 208 classified as cells. In some embodiments, a classified object may contain more than one cell (e.g., live cell mass 210), and the number of cells in the classified object may be counted and added to the total cell count. The number of cells in the live cell mass 210 may be identified, for example, by analyzing the intensity contour associated with the live cell mass 210. The centers of the cells in the live cell mass 210 may appear as bright spots in the image. The bright spots may appear as sharp peaks in the intensity contour at the center of each cell in the live cell mass 210. The number of peaks in the intensity contour of the live cell mass 212 may thereby be counted to identify the number of cells in the live cell mass 210.

[0033] FIG. 3 shows an exemplary process 300 for counting cells in a container. The process may be performed by a system including, for example, an imaging system configured to capture images of cells at different focal planes and a controller coupled to the imaging system configured to analyze the captured images, analyze the focused images, and estimate the number of cells in the focused images. The system may be implemented as a cell culture incubator or an automated cell counter, as shown in FIGS. 4 and 5 , respectively. As shown, process 300 includes act 302 of receiving cells in a container, act 303 of capturing focused images of the cells, and act 305 of estimating the number of cells using the focused images. Act 303 of capturing focused images of the cells may include act 304 of capturing an image of the cells, act 306 of determining the area of ​​the cells in the captured images, and act 308 of selecting one image as the focused image using the determined area. Act 305 of estimating cell number using the focused image may include act 310 of identifying objects in the focused image, act 312 of classifying the objects in the focused image, and act 314 of counting the number of objects classified as cells in the focused image.

[0034] In act 302, an imaging system may receive cells in a container. For example, the imaging system may receive cells at an imaging location (e.g., imaging location 405) so that the imaging system may capture images of the cells. In some embodiments, the cells in the container may be exposed to a chemical that selectively labels dead cells. The chemical may be a dye that selectively stains dead cells, such as trypan blue and propidium iodide. Labeling dead cells using a chemical may allow the controller to more easily distinguish dead cells from live cells by enhancing the contrast between them. Additionally (or alternatively), the imaging system may include an optical filter to further enhance the contrast between live and dead cells. Examples of such imaging systems are shown in FIGS. 6A and 6B.

[0035] In act 303, the controller may control the imaging system to capture a focused image (e.g., a focused brightfield image) of the cells in the vessel. The focused image may be, for example, an image in which the cells in the vessel are in focus. The focused image may be captured in any of a variety of ways. An exemplary process for capturing a focused image is shown in FIG. 3 by acts 304, 306, and 308.

[0036] In act 304, the controller may control the imaging system to capture multiple images of the cells in multiple different focal planes (e.g., capture a Z-stack). For example, the controller may control the imaging system to capture multiple bright field images in multiple different focal planes. The multiple focal planes may be evenly (or non-uniformly) spaced apart. In some embodiments, the multiple focal planes may be selected based on the particular type of cells being counted. For example, a focal plane above the top surface of the cells being imaged may be omitted from the multiple focal planes. In other embodiments, the multiple focal planes may be a fixed set of focal planes that are used regardless of the type of cells being counted.

[0037] In act 306, the controller may determine the area of ​​cells in the captured images. The area of ​​cells in each of the images may be identified, for example, by identifying cells (e.g., single cells) in the images and estimating the area of ​​the identified cells. Cells may be identified by separating the foreground from the background in each image and identifying objects in the foreground that have characteristics (e.g., shape, size, and / or color) of single cells. For example, a global threshold may be applied to the entire image to separate light pixels (background) from dark pixels (foreground). The global threshold may be identified, for example, using the Otsu thresholding algorithm. Once the global threshold is applied, a local threshold may be applied to a bounded region (e.g., a bounded rectangle) in the image that contains a contiguous set of dark pixels to fine-tune the delineation between the foreground and background. The local threshold may be identified, for example, by using the average intensity of pixel values ​​within a selected region as the threshold. Once the local threshold is applied, the area of ​​the background that is completely (or partially) surrounded by a continuous region of foreground pixels may be added to the foreground. The resulting continuous region in the foreground may be identified as an object. Objects having the characteristics (e.g., size, shape, and / or color) of a single cell may be used to calculate the area of ​​the cell. Other objects in the foreground may be completely ignored, thereby being filtered out. The area of ​​an identified single cell may be estimated, for example, by counting the number of pixels associated with the identified single cell and / or estimating the axial length of the identified single cell.

[0038] In act 308, the controller may use the determined area of ​​the cell to select one image from the multiple images (e.g., captured in act 304) as the focused image. For example, the controller may select the image with the cell with the smallest area as the focused image. In some embodiments, the controller may repeat acts 304 and / or 306 if the selected image does not meet one or more predetermined requirements (e.g., the area is above a threshold). For example, the controller may determine that the best image in the multiple images captured in act 304 is insufficient and repeat act 304, capturing a second multiple images in a different set of focal planes (relative to the set of focal planes associated with the second multiple images). The area of ​​the cell in the second multiple images may be identified in act 306, and the controller may select one image from the second multiple images as the focused image in act 308.

[0039] In act 305, the controller may estimate the number of cells in the focused image. The number of cells may be estimated, for example, using automatic image processing techniques. An exemplary process for estimating the focused image is shown in FIG. 3 by acts 310, 312, and 314.

[0040] In act 310, the controller may identify an object in the focused image. The controller may identify an object in the focused image by separating the background from the foreground of the focused image (e.g., in a manner similar or identical to that described in act 306) and identifying a contiguous region of pixels in the foreground (e.g., a portion of the foreground) as the object. The background may be separated from the foreground using, for example, edge detection techniques (thresholding and / or iterative thresholding).

[0041] In act 312, the controller may classify the identified objects in the focused image. The controller may classify the objects, for example, by identifying one or more features of the objects and providing the one or more features of the objects as input to a classifier. The classifier may be configured (e.g., trained) to identify a class to which the object belongs based on the input features. The particular set of classes that the classifier is configured to distinguish may vary based on the particular implementation. Exemplary classes include a single live cell class, a live cell clump class, a single dead cell class, a dead cell clump class, and a debris class.

[0042] The controller may identify any of a variety of characteristics of the object and use them for classification. Exemplary characteristics that may be identified include morphological features, light intensity features, and texture features. Morphological features may relate, for example, to the size and / or shape of the object. Exemplary morphological features include the contour area of ​​the object, the convex hull area of ​​the object, the ratio of the contour area of ​​the object to the convex hull area, the circularity of the object, and the ratio of the area of ​​the circumscribing rectangle around the object to the area of ​​the object. Light intensity features may relate, for example, to characteristics of the intensity values ​​of pixels comprising the object. Exemplary light intensity features include the average pixel intensity value of the brightest pixels within the object (e.g., the top 10 brightest pixels), gray value features of the object (e.g., the sum, mean, standard deviation, and variance of the gray value of the object), and optical density features of the object (e.g., the sum, mean, standard deviation, and variance of the optical density of the object). Texture features may relate, for example, to the appearance of the surface and / or cross-section of the object. Exemplary texture features include object entropy and object contrast.

[0043] The controller may employ any of a variety of classifiers and / or classification techniques to classify objects in the focused image. For example, a decision tree classifier may be used. As another example, a linear classifier (e.g., Fischer's linear decision classifier, logistic regression classifier, naive Bayes classifier, probit regression classifier, etc.) may be used. As yet another example, a Bayesian classifier (e.g., a Bayesian network or other graphic model-based classifier) ​​may be used. As yet another example, a neural network classifier (e.g., a single-layer neural network, a multi-layer neural network, a deep neural network, a recurrent neural network, a convolutional neural network, etc.) may be used. The classifier may be trained using training data including image features and corresponding counts manually determined by one or more technicians.

[0044] In act 314, the controller may count the number of objects classified as cells in the focused image. For example, the controller may count the number of objects classified as single live cells and the number of cells in each object classified as a live cell clump, resulting in a total number of live cells in the focused image. The number of dead cells may also be counted to identify the total number of (live and dead) cells in the focused image. The controller may count the number of live cells in a live cell clump in any of a variety of ways. For example, the controller may count the number of cells in a live cell clump, which may be identified, for example, by analyzing an intensity contour associated with the cell clump. The centers of cells in a live cell clump may appear as bright spots in the focused image. The bright spots may appear as sharp peaks in the intensity contour at the center of each cell in the clump. The number of peaks in the intensity contour of the live cell clump may thereby be counted to identify the number of cells in the live cell clump.

[0045] In some embodiments, only a portion of the cells in the container may be visible in an image captured by the imaging system (e.g., captured in act 304). In these embodiments, the system may divide the container into multiple sections and count the number of cells visible in each section by performing acts 303 and / or 305. Once the cells in each section have been counted, the total cell number may be determined by summing the cells in each section.

[0046] Various inventive concepts may be embodied as one or more processes, examples of which are provided. The acts performed as part of each process may be ordered in any suitable manner. Thus, although shown as sequential acts in illustrative embodiments, embodiments may be constructed in which acts are performed in an order different from that shown, which may include performing some acts simultaneously.

[0047] In some embodiments, the techniques described herein may be employed within a cell culture incubator. The cell culture incubator may be constructed to culture cells with little or no manual handling, thereby reducing or eliminating the possibility of cell contamination. An example of such a cell culture incubator is shown in FIG. 4 by cell culture incubator 400. Cell culture incubator 400 includes an incubator cabinet 409 having an interior chamber 408 for incubation of cells within one or more cell culture containers. Incubator cabinet 409 includes an exterior door 401 that opens and closes to allow communication between the external environment and incubator cabinet 409. In some embodiments, exterior door 401 opens and closes to allow communication between the external environment and interior chamber 408. Interior chamber 408 is configured to hold one or more cell culture containers. The one or more cell culture containers are stored within storage location 402. In some embodiments, storage location 402 is a freestanding structure. For example, storage locations 402 may be test tube or culture flask racks that can be removed from interior chamber 408 for loading and unloading of culture vessels. In some embodiments, storage locations 402 are affixed to a surface of interior chamber 408. For example, storage locations 402 may be a series of racks or shelves that are connected to a wall or floor of interior chamber 408 and therefore cannot be removed from incubator cabinet 409.

[0048] In some embodiments, cell culture incubator 400 includes a transfer device 403 for moving one or more cell culture vessels. Transfer device 403 may be affixed to any suitable surface of interior chamber 408. For example, transfer device 403 may be affixed to a top surface or ceiling of interior chamber 408. Alternatively, transfer device 403 may be affixed to a sidewall of interior chamber 408. In some embodiments, transfer device 403 is not affixed to a wall of interior chamber 408. For example, transfer device 403 may rest on a wheeled tripod or other mobile structure that can move around interior chamber 408.

[0049] In some embodiments, transfer device 403 moves one or more cell culture vessels from storage location 402 to an imaging location 405 in imaging system 410 or to a manipulation location 407 in manipulation system 411. Transfer device 403 can move one or more cell culture vessels from imaging location 405 to manipulation location 407 or from manipulation location 407 to imaging location 105. Once imaging or manipulation is complete, transfer device 403 moves one or more cell culture vessels from imaging location 405 or manipulation location 407 to storage location 402.

[0050] In some embodiments, the transfer device 403 may include one or more elements such as valves (e.g., electromagnetic or pneumatic valves), gears, motors (e.g., electric or stepper motors), stages (e.g., xy or xyz stages), pistons, brakes, cables, ball-screw assemblies, rack-and-pinion arrangements, grippers, arms, pivot points, joints, translation elements, or other mechanical or electrical elements. In some embodiments, the transfer device 403 may include one or more robotic elements. For example, the transfer device 403 may include a robotic arm capable of gripping, lifting, pushing, grasping, sliding, rotating, translating, releasing, raising, lowering, and / or tilting one or more cell culture vessels. In some cases, the transfer device 403 selectively and releasably grips one or more cell culture vessels. In some embodiments, the transfer device 403 may include an arm coupled to a mechanical gripper. For example, the arm may include a mechanical gripper at or near one end for releasably grasping a cell culture vessel and be fixedly coupled to a surface or element of the incubator at or near the other end. In some embodiments, the robotic arm includes a pivot point at which the mechanical gripper is coupled to the arm and one or more pivot and / or translation joints along the arm, allowing flexible rotation and translation of a portion of the arm. In this way, the robotic arm may access one or more cell culture vessels at different horizontal and vertical positions within the incubator cabinet (e.g., a storage array within an interior chamber).

[0051] In some embodiments, incubator cabinet 409 includes imaging location 405 and operating location 407. In some embodiments, imaging location 405 is located on a surface of interior chamber 408 opposite imaging device 404. In some embodiments, imaging location 405 is a platform, either freestanding or affixed to interior chamber surface 408. In some embodiments, the platform is movable. For example, a movable platform may be affixed to two or more rods that allow the platform to be moved left, right, forward, backward, up, or down relative to imaging device 404. In some embodiments, the movable platform is motorized.

[0052] In some embodiments, imaging system 410 may be configured to capture images of cells in a cell culture vessel when the vessel is at imaging location 408. For example, the imaging system may be configured to capture phase-contrast and / or bright-field images of the cells in the cell culture vessel. Imaging system 410 may include an imaging device 404 configured to measure light (e.g., transmitted or scattered light), color, morphology, and / or other detectable parameters. Imaging device 404 may be, for example, a monochrome imaging device, a red / green / blue (RGB) imaging device, a spectral imaging device, a fluorescence imaging device, and / or a multi-channel imaging device. In an embodiment, imaging system 410 includes one or more lenses, fibers, apertures, mirrors, light sources (e.g., lasers or lamps), or other optical elements. Imaging system 410 may be implemented, for example, as a microscope.

[0053] In some embodiments, the manipulator system 411 includes a manipulator 406 that manipulates cells in a cell culture vessel when the vessel is in the manipulation location 407. In some embodiments, the manipulator 406 has an array of needles, capillaries, pipettes, and / or micromanipulators. For example, the manipulator 406 may include a cell picker. In some embodiments, the manipulator 406 comprises one or more cell pickers. In some embodiments, the manipulator 406 may include a cell scraper that includes a scraping edge suitable for scraping and removing cells from a surface. In some embodiments, the scraping edge is a part of the cell scraper that can contact the surface of the cell culture vessel or other surface and is suitably configured to scrape material from the surface to clean the surface and / or scrape cells that adhere to the surface without substantially killing the cells, for example, by mechanically lysing the cells. In some embodiments, it is desirable that the scraping edge or scraping edge assembly be disposable to prevent cross-contamination between cell cultures. Thus, in some embodiments, the scraping edge or scraping edge assembly is disposable.

[0054] In some embodiments, cell culture incubator 400 includes a controller 412 configured to control the operation of one or more components in cell culture incubator 400, such as imaging system 410, manipulator system 411, and / or transfer device 403. Controller 412 may be configured to perform one or more acts in the manner described above. For example, controller 412 may provide instructions to transfer device 403 to cause the transfer device to move a cell culture container to imaging location 405 and provide instructions to imaging system 410 to capture images of cells in the cell culture container.

[0055] Aspects of the present disclosure relate to incubators and methods for culturing, manipulating, and / or monitoring cells under controlled conditions (e.g., aseptic and / or sterile conditions). In some embodiments, cell cultures are grown in a culture vessel within an incubator of the present disclosure. As used herein, a "cell culture vessel" is a device including a housing and one or more chambers for culturing cells. In some embodiments, the housing is a frame. The frame may be coupled to a lid. The one or more chambers may contain cell culture medium, including one or more membranes. In some embodiments, the cell culture vessel may contain nutrients to promote cell growth. In certain embodiments, the cell culture vessel may completely enclose one or more cells or groups thereof. The housing of the cell culture vessel may include one or more pores or openings to allow gas transfer between the cell culture vessel and its surrounding environment. In certain embodiments, the cell culture vessel includes a transparent or optically clear window. For example, a lid coupled to the housing of the cell culture vessel may include an optically clear portion for viewing the cells, e.g., using an imaging system. In some embodiments, the cell culture vessel includes one or more portions that are substantially non-reflective.

[0056] The cell culture vessels may be configured for culturing different types of cells, including eukaryotic or prokaryotic cells. In some embodiments, the cells are mammalian cells (e.g., human cells, canine cells, bovine cells, ovine cells, feline cells, or rodent cells such as rabbit, mouse, or rat cells). In some embodiments, the cells are insect cells, avian cells, microbial cells (e.g., yeast cells such as Saccharomyces cerevisiae, Kluyveromyces lactis, or Pischia pastoris cells, or bacterial cells such as Escherichia coli, Bacillus subtilis, or Corynebacterium cells), insect cells (e.g., Drosophila cells or Sf9 or Sf21 cells), plant cells (e.g., algal cells), or any other type of cell.

[0057] In some embodiments, cell culture vessels may be pre-kitted with one or more desired reagents for a particular purpose, e.g., to grow cells, differentiate cells, expose cells to particular assay conditions, etc. In some embodiments, the pre-kitted cell culture vessels include reagents (e.g., cell growth medium, growth factors, selection agents, labeling agents, etc.) useful for performing a particular experiment on cell cultures prior to the experiment. Pre-kitted cell culture vessels may expedite experimental protocols by providing vessels ready for cell culture without requiring the addition of reagents. For example, progenitor cells from a patient may be added to a cell culture vessel pre-kitted with reagents for cell differentiation for the purpose of expanding a population of differentiated cells for autologous cell therapy. Pre-kitted cell culture vessels can be stored at any appropriate temperature, as determined by the recommended storage parameters of the reagents in the pre-kitted cell culture vessels. In some embodiments, the pre-kitted cell culture storage vessels are stored at a temperature of about -80°C to about 37°C prior to use. In some embodiments, the pre-kitted cell culture storage vessels are stored at a temperature of about −80° C. to about −20° C. prior to use. In some embodiments, the pre-kitted cell culture storage vessels are stored at a temperature of about −20° C. to about 4° C. prior to use. In some embodiments, the pre-kitted cell culture storage vessels are stored at a temperature of about 4° C. to about 37° C. prior to use. In some embodiments, the pre-kitted cell culture vessels are disposable. In some embodiments, the pre-kitted cell culture vessels are reusable and / or refillable.

[0058] In some embodiments, the cells are cultured to produce a natural product (e.g., taxol, pigments, fatty acids, biofuels, etc.). In some embodiments, the cells are cultured to express a recombinant product (e.g., a recombinant protein product such as an antibody, hormone, growth factor, or other therapeutic peptide or protein). In some embodiments, the cells are expanded and / or differentiated for therapeutic use, such as implantation into a subject (e.g., a human subject) to provide or complement a missing or deficient cell, tissue, or organ function within the subject.

[0059] In some embodiments, the cells are derived from immortalized cell lines. Non-limiting examples of cell lines include human cells, such as HeLa cells, prostate cancer cells (e.g., DU145, PC3, and / or Lncap cells), breast cancer cells (e.g., MCF-7, MDA-MB-438, and / or T47D cells), acute myeloid leukemia cells (e.g., THP-1 cells), glioblastoma cells (e.g., U87 cells), neuroblastoma cells (e.g., SHSY5Y cells), bone cancer cells (e.g., Saos-2 cells), and chronic myeloid leukemia cells (e.g., KBM-7 cells). In some embodiments, the cell line includes a primate cell line, a rodent cell line (e.g., a rat or mouse cell line), a canine cell line, a feline cell line, a Zebrafish cell line, a Xenopus cell line, a plant cell line, or any other cell line. In some embodiments, the cells are human 293 cells (eg, 293-T or HEK293 cells), murine 3T3 cells, Chinese hamster ovary (CHO) cells, CML T1 cells, or Jurkat cells.

[0060] In some embodiments, the cells are primary cells, feeder cells, or stem cells. In some embodiments, the cells are isolated from a subject (e.g., a human subject). In some embodiments, the cells are primary cells isolated from a tissue or biopsy sample. In some embodiments, the cells are hematopoietic cells. In some embodiments, the cells are stem cells, e.g., embryonic stem cells, mesenchymal stem cells, cancer stem cells, etc. In some embodiments, the cells are isolated from a tissue or organ (e.g., a human tissue or organ), including, but not limited to, solid tissues and organs. In some embodiments, the cells can be isolated from placenta, umbilical cord, bone marrow, liver, blood, including umbilical cord blood, or any other suitable tissue. In some embodiments, patient-specific cells are isolated from a patient for culture (e.g., for cell expansion and optional differentiation) and subsequent re-implantation into the same or a different patient. Thus, in some embodiments, cells grown in the incubators disclosed herein may be used for allogeneic or autologous therapy. In some embodiments, cells grown in the incubators disclosed herein may be genetically modified, expanded, and reintroduced into a patient for purposes of providing immunotherapy (e.g., delivery of chimeric antigen receptor therapy (CAR-T) or CRISPR / Cas modified cells).

[0061] In some embodiments, the primary cell culture comprises epithelial cells (e.g., corneal epithelial cells, breast epithelial cells, etc.), fibroblasts, myoblasts (e.g., human skeletal muscle myoblasts), keratinocytes, endothelial cells (e.g., microvascular endothelial cells), medullary cells, smooth muscle cells, hematopoietic cells, placental cells, or a combination of two or more thereof.

[0062] In some embodiments, the cell is a recombinant cell (e.g., a hybridoma cell or a cell expressing one or more recombinant products). In some embodiments, the cell is infected with one or more viruses.

[0063] In some embodiments, cells are isolated from tissues or biological samples for ex vivo culture in an incubator provided herein. In some embodiments, cells (e.g., white blood cells) are isolated from blood. In some embodiments, cells are released from tissues or biological samples using physical and / or enzymatic disruption. In some embodiments, one or more enzymes, such as collagenase, trypsin, or pronase, are used to digest the extracellular matrix. In some embodiments, the tissue or biological sample is placed in culture medium (e.g., with or without physical or enzymatic disruption), and the released cells are grown in the culture medium and can be isolated for further culture.

[0064] As used herein, cell culture refers to a procedure for maintaining and / or growing cells under controlled conditions (e.g., ex vivo). In some embodiments, cells are cultured under conditions to promote cell growth and replication, conditions to promote expression of a recombinant product, conditions to promote differentiation (e.g., into one or more tissue-specific cell types), or a combination of two or more thereof.

[0065] In some embodiments, the cell culture vessel is configured for culturing cells in suspension. In some embodiments, the cell culture vessel is configured for culturing adherent cells. In some embodiments, the cell culture vessel is configured for 2D or 3D cell culture. In some embodiments, the cell culture vessel comprises one or more surfaces or microcarriers to support cell growth. In some embodiments, these are coated with extracellular matrix components (e.g., collagen, fibrin, and / or laminin components) to increase adhesive properties and provide other signals required for growth and differentiation. In some embodiments, the cell culture vessel comprises one or more synthetic hydrogels, such as polyacrylamide or polyethylene glycol (PEG) gels, to support cell growth. In some embodiments, the cell culture vessel comprises a solid support with embedded nutrients (e.g., gel or algae, for example, for certain bacterial or yeast cultures). In some embodiments, the cell culture vessel comprises a liquid culture medium.

[0066] In some embodiments, cells are cultured in any suitable culture medium. Different culture media with different ranges of pH, glucose concentration, growth factors, and other supplements can be used for different cell types or different applications. In some embodiments, custom or commercially available cell culture media can be used, such as Dulbecco's Modified Eagle Medium, Minimum Essential Medium, RPMI Medium, HA or HAT Medium, or other media available from Life Technologies or other commercial sources. In some embodiments, the cell culture medium contains serum (e.g., fetal bovine serum, calf serum, horse serum, porcine serum, or other serum). In some embodiments, the cell culture medium is serum-free. In some embodiments, the cell culture medium contains human platelet lysate (hPL). In some embodiments, the cell culture medium includes one or more antibiotics (e.g., actinomycin D, ampicillin, carbenicillin, cefotaxime, fosmidomycin, gentamicin, kanamycin, neomycin, penicillin, penicillin-streptomycin, polymyxin B, streptomycin, tetracycline, or any other suitable antibiotic or any combination of two or more thereof. In some embodiments, the cell culture medium includes one or more salts (e.g., balanced salts, calcium chloride, sodium chloride, potassium chloride, magnesium chloride, etc.). In some embodiments, the cell culture medium comprises sodium bicarbonate. In some embodiments, the cell culture medium comprises one or more buffering agents (e.g., HEPES or other suitable buffers). In some embodiments, one or more supplements are included. Non-limiting examples of supplements include reducing agents (e.g., 2-mercaptoethanol), amino acids, cholesterol supplements, vitamins, transferrin, detergents (e.g., non-ionic detergents), CHO supplements, primary cell supplements, yeast solution, or any combination of two or more thereof.In some embodiments, one or more growth or differentiation factors are added to the cell culture medium. Growth or differentiation factors (e.g., WNT-based proteins, BMP-based proteins, IGF-based proteins, etc.) can be added individually or in combination, for example, as a differentiation mixture containing different factors that induce differentiation into specific lineages. Growth or differentiation factors and other aspects of the liquid medium can be added using an automated liquid handler integrated as part of the incubator provided herein.

[0067] In some aspects, the incubators and methods described herein provide and maintain the appropriate temperature and gas mixture for cell growth. It should be understood that cell growth conditions vary for different cell types, and the incubators described herein can be programmed to maintain different conditions. In some embodiments, conditions of about 37°C and 5% CO2 are used for mammalian cells.

[0068] In some embodiments, the devices and methods described herein are used to monitor or evaluate culture media for nutrient depletion, changes in pH, changes in temperature accumulation of apoptotic or necrotic cells, and / or cell density. In some embodiments, the devices and methods described herein are used to modify or change culture media or conditions and / or pass cell cultures when appropriate. In some embodiments, these procedures are automated.

[0069] In some embodiments (e.g., for adherent cell cultures), the culture medium can be directly removed by aspiration and replaced with new medium. In some embodiments (e.g., for non-adherent / suspension cultures), a medium change can involve centrifuging the cell culture, removing the old culture medium, and replacing it with new medium. In some embodiments, the centrifuge is located within the interior chamber of the incubator. In some embodiments, the culture vessel allows for continuous medium exchange. In some embodiments, the incubators described herein may include one or more components that can be used to process, exchange, supply, and / or maintain different aspects of the culture medium and support the cells. The incubator may include a reservoir containing waste medium and / or a reservoir containing new medium. Such reservoirs may be located in a refrigerator inside the incubator or in a refrigerated section of the incubator (e.g., for temporary storage). In some embodiments, one or more reservoirs are provided outside the incubator, and tubing is provided in and out of the incubator space to supply or withdraw from a liquid handler unit (e.g., a liquid handle unit with an aspirator) or temporary reservoirs within the incubator, facilitating cell feeding, medium changes, and other related needs. For suspension cells, a device (e.g., a centrifuge to facilitate cell fractionation) may be provided within the incubator to separate cells from waste medium and facilitate automated medium changes as part of the incubators provided herein. In some embodiments, this document provides a system comprising a cell culture incubator coupled to a computer that can automatically monitor and adjust cell culture conditions for optimal growth of the cell culture.

[0070] In some embodiments, cells are passaged in an incubator cabinet as described herein. In some embodiments, the cell culture is split and a subset of the cell culture is transferred to a new culture vessel for further growth. In some embodiments (e.g., for adherent cell culture), the cells are detached from the surface (e.g., mechanically, e.g., using gentle scraping, and / or enzymatically, e.g., using trypsin-EDTA or one or more other enzymes) prior to being transferred to the new culture vessel. In some embodiments (e.g., for suspension cell culture), a small volume of the cell culture is transferred to the new culture vessel.

[0071] In some embodiments, the cell culture is manipulated in other ways while being cultured in the incubator cabinet of the incubator herein. For example, the cell culture can be transfected with nucleic acid (e.g., DNA or RNA) or exposed to viral infection (e.g., using recombinant viral particles to deliver DNA or RNA) while remaining in the incubator cabinet of the incubator provided herein.

[0072] It should be understood that aseptic techniques can be used to prevent or minimize contamination of cell cultures during growth and manipulation. In some embodiments, equipment used for cell culture (e.g., pipettes, fluid handling devices, manipulation devices, other automated or robotic devices, etc.) is sterilized using an appropriate technique. Non-limiting techniques include heat exposure (e.g., autoclaving), surface disinfection (e.g., using alcohol, bleach, or other disinfectants), irradiation, and / or exposure to disinfectant gases (e.g., ozone, hydrogen peroxide, etc.), as described herein. In some embodiments, culture media is sterilized using an appropriate technique. Non-limiting techniques include heat exposure (e.g., autoclaving), antibacterial / antiviral treatment, filtration, and / or irradiation.

[0073] In some embodiments, cell culture operations are performed under aseptic conditions, eg, in an environment (eg, an incubator chamber) that is disinfected, air filtered, and free of potential contaminants.

[0074] In some embodiments, the cell cultures are grown and maintained under GMP-compliant conditions, including those involving the use of GMP-compliant media or GMP-compliant liquid handling equipment. In some cases, the cell cultures are grown and maintained by practicing methods in conjunction with standard operating procedures (SOPs).

[0075] In some embodiments, cell cultures can be monitored and / or evaluated to detect contamination. In some embodiments, contamination with cells from different types of microorganisms can be detected. In some embodiments, contamination of mammalian cell cultures with mycoplasma, bacteria, yeast, or viruses can be detected using any suitable technique. In some embodiments, cell culture contamination can be detected by assaying a change or rate of change in one or more culture properties, such as pH, turbidity, etc., that are characteristic of the contamination (e.g., bacterial or yeast) and not of the cells (e.g., mammalian cells) being grown in the culture. In some embodiments, one or more molecular detection assays (e.g., PCR, ELISA, RNA labeling, or other enzymatic techniques) or cell-based assays can be used to detect contamination (e.g., mycoplasma, bacterial, yeast, viral, or other contamination).

[0076] In some embodiments, cell cultures can be monitored and / or assessed to detect contamination with cells of a similar type (e.g., a human cell line contaminated with a different human cell or a different mammalian cell). In some embodiments, the cell culture and its potential contamination can be assessed using DNA sequencing or DNA fingerprinting (e.g., short tandem repeat - STR-fingerprinting), isozyme analysis, human lymphocyte antigen (HLA) determination, chromosome analysis, karyotyping, cell morphology, or other techniques.

[0077] In some embodiments, cells generated using the incubators or methods described herein can be frozen and preserved for later use and / or transport. In some embodiments, cells are mixed with a cryopreservation composition after growth and / or differentiation and prior to freezing. The cryopreservation composition can be added to a cell culture container, or the cells can be transferred from a cell culture container to a cryopreservation container along with the cryopreservation composition. Non-limiting examples of cryoprotectants that may be included in the cryopreservation composition include DMSO, glycerol, PEG, sucrose, trehalose, and dextrose. In some embodiments, a freezing device may be provided as a component of the incubator to facilitate freezing of cells isolated from the cell culture. For example, one or more freezing devices may be located within an interior chamber and / or integrated into the incubator cabinet (e.g., within a wall of the incubator cabinet).

[0078] In some embodiments, this document relates to incubators and methods for culturing, manipulating, and / or monitoring cells under controlled conditions (e.g., under aseptic and / or sterile conditions). In some embodiments, the cell culture incubator includes an incubator cabinet having an interior chamber for incubating cells in one or more cell culture containers. In some cases, in addition to an interior door from a transfer chamber to the interior chamber, the incubator includes at least one exterior door (e.g., one, two, three, four, or more exterior doors) that opens directly to the interior chamber from the external environment and provides alternative access to the interior chamber, for example, during time periods when the incubator is not operating, such as during incubator maintenance. In some embodiments, the incubator includes a storage location within the interior chamber for storing one or more cell culture containers.

[0079] As used herein, an "incubator cabinet" is an enclosure that includes one or more chambers configured to hold one or more cell culture vessels. In some embodiments, an incubator cabinet includes a transfer chamber and an internal chamber, either or both of which are configured to hold one or more cell culture vessels.In some embodiments, the incubator includes one or more gas sources (e.g., gas cylinders or ozone generators), tubing (e.g., for delivering one or more liquids or gases, such as water, distilled water, deionized water, cell culture media, air, carbon dioxide, ozone, and oxygen), air flow mechanisms (e.g., valves, release valves, pinholes, gas regulators, and mass flow regulators), pressure mechanisms (e.g., pumps such as dry scroll pumps, rotary pumps, momentum transfer pumps, diffusion pumps, or diaphragm pumps; suction tubing; vacuum systems; and air blowers), environmental monitors and controls (e.g., gas sensors and / or monitors for sensing and / or controlling concentrations of gases such as carbon dioxide, oxygen, and ozone; heat sources or sinks; temperature monitors and controls; humidity monitors; gas scrubbers; air filters; instrumentation for measuring particulate matter; pressure gauges; and flow meters), doors (e.g., openings or panels), windows (e.g., glass, plastic, composite, etc., for viewing the interior area of ​​the incubator). The incubator cabinet may include one or more other elements, such as optical windows made of composites or other substantially transparent materials, ports (e.g., allowing for the introduction or removal of one or more gases or liquids), light sources (e.g., lamps, bulbs, lasers, and diodes), optical elements (e.g., microscope objectives, mirrors, lenses, filters, apertures, wave plates, windows, polarizers, fibers, beam splitters, and beam combiners), imaging elements (e.g., cameras, barcode readers), electrical elements (e.g., circuits, cables, power cords, and power sources such as batteries, generators, and DC or AC power supplies), controllers, mechanical elements (e.g., motors, wheels, gears, robotic elements, and actuators such as pneumatic actuators, electromagnetic actuators, motors with cams, piezoelectric actuators, and motors with lead screws), and control elements (e.g., spin wheels, buttons, keys, toggles, switches, cursors, screws, dials, screens, and touch screens). In some embodiments, one or more of these other elements are part of the incubator but are external to the incubator cabinet.In some embodiments, one or more of these other elements are contained within the incubator cabinet.

[0080] In some embodiments, the incubators or incubator cabinets provided herein are rectangular parallelepiped shaped. In some embodiments, the incubators or incubator cabinets provided herein are 1 foot 2 ~16 feet 2 In some embodiments, the incubators or incubator cabinets provided herein have a rectangular footprint within a range of up to about 1 ft 2 , 2 feet 2 , 3 feet 2 , 4 feet 2 , 5 feet 2 , 6 feet 2 , 7 feet 2 , 8 feet 2 , 9 feet 2 , 10 feet 2 , 11 feet 2 , 12 feet 2 , 13 feet 2 , 14 feet 2 , 15 feet 2 , or 16 feet 2 In some embodiments, the incubators or incubator cabinets provided herein have a rectangular footprint of 1 ft. 3 ~100 feet 3 In some embodiments, the incubators or incubator cabinets provided herein have a total chamber volume within the range of up to about 1 ft 3 , 5 feet 3 , 10 feet 3 , 25 feet 3 , 50 feet 3 , or 100 feet 3 In some embodiments, the incubators or incubator cabinets provided herein have a chamber volume of 0.09 m 2 ~1.78m 2In some embodiments, the incubators or incubator cabinets provided herein have a rectangular footprint of up to about 0.1 m 2 , 0.2m 2 , 0.3m 2 , 0.4m 2 , 0.5m 2 , 0.6m 2 , 0.7m 2 , 0.8m 2 , 0.9m 2 , 1.0m 2 , 1.1m 2 , 1.2m 2 , 1.3m 2 , 1.4m 2 , 1.5m 2 , 1.6m 2 , or 1.7m 2 In some embodiments, the incubators or incubator cabinets provided herein have a rectangular footprint of 0.03 m 3 ~3m 3 In some embodiments, the incubators or incubator cabinets provided herein have a total chamber volume in the range of up to about 0.03 m 3 , 0.1m 3 , 0.3m 3 , 1m 3 , or 3m 3 The chamber volume is

[0081] As used herein, a "storage location" refers to a location (e.g., within an incubator cabinet) where one or more cell culture vessels are stored. For example, one or more cell culture vessels may be stored in a storage location and later transported to a different location (e.g., an imaging location). A storage location may be located within an interior chamber cabinet of an incubator. A storage location may be configured to store multiple cell culture vessels. For example, a storage location may include one or more storage arrays, racks, shelves, sorters, organizers, trays, slots, or other positions or mechanisms. In some embodiments, a storage location may be configured to store cell culture vessels horizontally, while in other embodiments, it may be configured to store cell culture vessels vertically. For example, a storage location may include multiple slots for receiving cell culture vessels stacked vertically over one another. A storage location may be configured to hold 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 100, or any other number of cell culture vessels. In some embodiments, a storage location may be configured to hold more than 100 cell culture vessels. In some embodiments, a storage location may include a mechanism for moving one or more storage arrays, racks, shelves, bins, organizers, trays, slots, or other positions or mechanisms. For example, a storage location may include one or more motors and movable stages (e.g., xy or xyz stages) to move a storage rack from one position within the internal chamber to another position within the internal chamber, e.g., to facilitate access to one or more cell culture vessels stored within different locations. In some embodiments, an incubator cabinet may include one or more cell culture vessel transport devices for moving one or more cell culture vessels.

[0082] A storage location may be configured to securely hold or receive one or more cell culture vessels. For example, one or more components of a storage location may include one or more locking mechanisms having one or more adhesive, magnetic, electrical, and / or mechanical components (e.g., snaps, fasteners, locks, catches, gaskets, O-rings, septa, springs, and other engagement members). In some embodiments, a storage location and / or cell culture vessel may include one or more grooves or recesses and / or may involve molded plastic pieces. For example, a cell culture vessel may include one or more protruding features (e.g., rims or knobs) molded for insertion into one or more corresponding grooves, holes, or recesses in the storage location. In some cases, a cell culture vessel may include one or more grooves, holes, or recesses molded to fit into one or more corresponding protruding features in the storage location.

[0083] As used herein, a "fiducial mark" refers to a feature that facilitates alignment of one or more components. In some embodiments, the fiducial mark may include one or more hole openings through the fluorescent medium or printed or embossed fluorescent material. In other embodiments, the fiducial mark may include a grid, line, or symbol. In some embodiments, one or more cell culture vessels include one or more fiducial marks to facilitate alignment of the one or more cell culture vessels with an imager.

[0084] In some embodiments, the incubator cabinet is single-walled. In some embodiments, the incubator is double-walled. In some embodiments, insulation is provided between the double walls of the incubator cabinet to control heat loss from the incubator cabinet and facilitate temperature control within the incubator cabinet. In some embodiments, the outer wall of the incubator cabinet comprises sheet metal, e.g., 14-20 cold-rolled steel. In some embodiments, the inner wall (e.g., chamber surface) of the incubator cabinet comprises electropolished stainless steel. In some embodiments, the inner wall (e.g., chamber surface) of the incubator cabinet comprises a corrosion-resistant material, such as titanium, cobalt-chromium, tantalum, platinum, zirconium, niobium, stainless steel, and alloys thereof. However, in some embodiments, the chamber surface of the incubator cabinet comprises a polymeric material, such as polytetrafluoroethylene (PTFE), or a polymeric material known under the trade name Parylene. In some embodiments, the chamber surface may have antimicrobial properties, such as copper or silver or antimicrobial compounds incorporated into a polymeric surface coating.

[0085] In some embodiments, the environment inside the incubator is controlled by a control system, which may be configured to control the temperature, humidity, carbon dioxide, oxygen, and other gaseous components (e.g., sterilizing gases such as ozone and hydrogen peroxide) inside the incubator (e.g., within one or more internal chambers). In some embodiments, the control system separately controls the environmental conditions (e.g., temperature, humidity, carbon dioxide, oxygen, and other gaseous components) within each internal chamber. For example, to protect sensitive mechanical, electronic, and optical components, the humidity of an internal chamber may be maintained at a lower level than an internal chamber having a storage location. In some embodiments, the incubator further comprises a monitoring system with predetermined sensors. Examples of monitoring devices include, but are not limited to, an oxygen monitor, a carbon dioxide monitor, an ozone gas detector, a hydrogen peroxide monitor, and a multi-gas monitor. For example, in some embodiments, the incubator advantageously includes multiple sensors responsive to different parameters related to cell growth, which may include temperature, air purity, contamination levels, pH, humidity, N2, CO2, O2, and light. Using the present monitoring system, parameters within the incubator can be measured over the duration of the culture or process using sensors. In some embodiments, the parameters measured by the sensors are transmitted by the monitoring system over a line to a computer-controlled monitoring and control system for further processing, as discussed elsewhere herein.

[0086] In some embodiments, an environmental monitoring system can be used in conjunction with the incubators described herein. In some embodiments, one or more sensors can be associated with the incubator (e.g., fitted within the incubator cabinet) that provide measurements of temperature, air composition (e.g., CO concentration, O concentration, etc.), and / or system humidity. In some embodiments, one or more such sensors can be incorporated as part of the incubator (e.g., attached to, integral with, or otherwise connected to an interior wall or door of the incubator). In some cases, one or more sensors can be positioned in any suitable location outside or inside the incubator cabinet (e.g., attached within the transfer chamber and / or interior chamber, e.g., to an interior wall and / or upper or lower interior surface).

[0087] In some embodiments, gas sensors are provided that can provide real-time readings of the concentration of a gas in contact with the sensor (e.g., the gas in the cabinet or the ambient air) in percent, parts per million, or any other standard units. Gas sensors for use in the methods and incubators provided herein include CO2 sensors, O2 sensors, N2 sensors, ozone gas detectors, hydrogen peroxide monitors, multi-gas monitors, and CO2 sensors. Such sensors are available from several commercial sources. In some cases, the environment of the incubator may be modulated or controlled based on information provided by the sensors described herein. For example, the level of CO2 in the incubator may be increased in response to an indication from the CO2 sensor that a lower than desired concentration of CO2 is present in the incubator.

[0088] In some embodiments, one or more heating or cooling elements can be incorporated into the incubator (e.g., on the interior surface of the cabinet or door and / or integrated into one or more of the cabinet walls and / or base) for the purpose of controlling the temperature within the incubator. In some embodiments, the heating elements can be used to thaw liquids, such as cell culture media or other reagents. In some embodiments, one or more air or oxygen sources, carbon filters, and / or one or more humidification or dehumidification systems are connected to the incubator and configured to control the levels of oxygen, carbon dioxide, and / or humidity within the incubator (e.g., in response to signals from one or more sensors within or attached to the incubator).

[0089] In some embodiments, the incubator may include one or more light sources (e.g., incandescent bulbs, LEDs, UV, or other light sources). These may be installed within the incubator to illuminate areas within the cabinet. In some embodiments, culture system operation is monitored using a camera or other light-sensitive device, which may be installed within or outside the incubator. In some embodiments, the light source is a germicidal light source. For example, a UV lamp may be located within the transfer chamber and / or the interior chamber of the incubator described herein.

[0090] In some embodiments, the incubator includes a transparent object (e.g., a window) that allows visible light or other wavelengths of light from within the incubator to be detected by a camera or other light-sensitive device installed outside the incubator. In some embodiments, the interior surface of the transparent object can be wiped (e.g., from the inside of a cabinet) to prevent or remove condensation that may accumulate on the interior surface (e.g., due to humid air inside an air incubator) and interfere with system monitoring. In some embodiments, the surface can be wiped by a wiper automatically controlled by a controller.

[0091] As used herein, a "door" is an element that, when open, allows communication between two or more environments or areas and, when closed, prevents communication between two or more environments or areas. The door may be of any type, such as a sliding door, pocket door, swing door, hinged door, revolving door, pivot door, or folding door. The door may be operated manually, mechanically, or electrically. For example, an operator may open or close the door by manually grasping, pulling, pushing, and / or otherwise physically interacting with the door or an element thereof (e.g., a handle), or by operating a mechanical control (e.g., a button, toggle, spin wheel, key, switch, cursor, screw, dial, screen, or touch screen). In some embodiments, the door may be controlled by an electrical or digital control, such as by a controller. The door may be an automatically opening door. For example, the door may include a sensor, such as a pressure, infrared, motion, or remote sensor, that detects whether the door is open or closed and / or controls when the door opens or closes. The doors may be opened mechanically, pneumatically, electrically, or by other means. In some embodiments, one or more doors may include one or more locking mechanisms. In certain circumstances, one or more doors include one or more interlocks (e.g., mechanical interlocks such as pins, bars, or locks, or electrical interlocks such as switches) to prevent the one or more doors from opening at undesired times (e.g., when one or more chambers are open to the outside environment).

[0092] In some embodiments, the incubator (e.g., the interior chamber and / or transfer chamber of the incubator cabinet) includes one or more windows and / or doors that, when closed, are sealed and maintain sterility (e.g., after one or more chambers of the incubator have been sterilized). In some embodiments, each seal in the incubator cabinet is airtight up to a threshold level of pressure (e.g., up to 1 atm). In some embodiments, a gasket is provided to ensure a desired level of sealing ability. In general, a "gasket" is generally understood as a mechanical seal that fills the space between two objects to prevent leakage between the two objects while under compression. Gaskets are generally produced by cutting from sheet materials such as gasket paper, rubber, silicone, metal, cork, felt, neoprene, nitrile rubber, fiberglass, or plastic polymers (such as polychlorotrifluoroethylene). It is often desirable for gaskets to be made from a material that provides some yield so that they can deform and tightly fill the space designed to contain any slight irregularities. In some embodiments, the gasket can be used in conjunction with a sealant applied directly to the gasket surface to function properly. In some embodiments, the gasket material can include closed-cell neoprene foam, which does not react with carbon dioxide or ozone.

[0093] As used herein, a "transfer device for moving one or more items" refers to a device that can transfer one or more items from a first location to a second location. In some embodiments, the one or more items are one or more cell culture vessels. In other embodiments, the one or more items are useful for maintenance of one or more cell culture vessels, including, but not limited to, pipettes, capillaries, liquids (e.g., cell culture medium), nutrients, and other materials. In certain embodiments, a transfer device may transfer one or more items to or from multiple locations within an incubator. For example, a transfer device may be used to move a pipette to a maintenance location within an internal chamber for maintenance of one or more cell culture vessels. In some embodiments, an incubator includes more than one transfer device for moving one or more items (e.g., two or more separate transfer devices for transferring items between and within chambers).

[0094] The transfer device may include one or more elements such as valves (e.g., electromagnetic or pneumatic valves), gears, motors (e.g., electric or stepper motors), stages (e.g., xy or xyz stages), pistons, brakes, cables, ball-screw assemblies, rack-and-pinion arrangements, grippers, arms, pivot points, joints, translation elements, or other mechanical or electrical elements. In some embodiments, the transfer device may include one or more robotic elements. For example, the transfer device may include a robotic arm capable of gripping, lifting, pushing, grasping, sliding, rotating, translating, releasing, raising, lowering, and / or tilting one or more items (e.g., pipettes). In preferred embodiments, the transfer device selectively and releasably grips one or more pipettes. In certain embodiments, the transfer device may include an arm coupled to a mechanical gripper. For example, the arm may include a mechanical gripper at or near one end for releasably grasping a pipette and be fixedly coupled to a surface or element of the incubator at or near the other end. In some embodiments, the robotic arm includes a pivot point at which the mechanical gripper is coupled to the arm and one or more pivot and / or translation joints along the arm, allowing flexible rotation and translation of portions of the arm. In this way, the robotic arm may access one or more items (e.g., pipettes) at different horizontal and vertical locations within the incubator (e.g., a storage array within an internal chamber).

[0095] As used herein, a "cell culture vessel transfer device" refers to a device capable of transferring one or more cell culture vessels from a first location to a second location. In certain embodiments, the transfer device may transfer one or more items to or from multiple locations within an incubator. For example, the cell culture vessel transfer device may be used to move a cell culture vessel from a transfer chamber to an internal chamber and / or from a storage location to an imaging location. In some embodiments, the incubator includes more than one transfer device (e.g., separate means for transferring items between and within chambers) for moving one or more items. The cell culture vessel transfer device may include one or more elements such as valves (e.g., electromagnetic or pneumatic valves), gears, motors (e.g., electric or stepper motors), stages (e.g., xy or xyz stages), pistons, brakes, cables, ball-screw assemblies, rack-and-pinion arrangements, grippers, arms, pivot points, joints, translation elements, or other mechanical or electrical elements. In some embodiments, the cell culture vessel transfer device may include one or more robotic elements. For example, a cell culture vessel transfer device may include a robotic arm capable of gripping, lifting, pushing, grasping, sliding, rotating, balancing, releasing, raising, lowering, and / or tilting one or more cell culture vessels. In preferred embodiments, the cell culture vessel transfer device selectively and releasably grips one or more cell culture vessels. In certain embodiments, the cell culture vessel transfer device may include an arm coupled to a mechanical gripper. For example, the arm may include a mechanical gripper at or near one end for releasably gripping a cell culture vessel and be fixedly coupled to a surface or element of an incubator at or near the other end. In some embodiments, the robotic arm includes a pivot point at which the mechanical gripper couples to the arm and one or more pivot and / or translation joints along the arm, allowing flexible rotation and translation of a portion of the arm.In this manner, the robotic arm may access one or more cell culture vessels at different horizontal and vertical positions within the incubator (eg, a storage array within an interior chamber).

[0096] In some embodiments, the transfer device comprises a robotic arm. In some embodiments, the robotic arm comprises a platform within the incubator cabinet that can move along rails or conveyors that extend in various directions along the interior surfaces (e.g., interior walls, base, etc.) of the incubator cabinet. In some embodiments, the incubator cabinet may be configured with more than one (e.g., two, three, four, or five or more) robotic arms to increase instrument throughput and provide redundancy in case of failure of one of the robotic arms.

[0097] In some embodiments, the transfer device may further include a gripper assembly coupled to the robotic arm. In some embodiments, the gripper assembly includes one or more grippers mounted at or near the end of the robotic arm, each gripper having two or more (e.g., three, four, five, or more) gripper fingers. In some embodiments, each of the gripper fingers of the robotic arm has a groove, friction plate, rubber pad, or other gripping surface. The gripping surface may enable the fingers to grip and transport various types of containers (e.g., culture vessels) within the cabinet. In some embodiments, the robotic arm may have an absolute encoder coupled to either the gripper assembly or the platform, or a separate absolute encoder for each gripper assembly or platform, to determine whether the robotic arm is in a position to safely return home (e.g., returned to a resting or storage configuration and / or the origin of a location or operating coordinate system) without hitting an obstacle.

[0098] In some embodiments, in some situations it may be desirable for the reach of the robotic arm not to extend to certain areas of the incubator cabinet, so the robotic arm may instead reach these locations by, for example, moving along an axis (e.g., x-axis, y-axis) and inserting or removing containers into or from a shuttle or conveyor belt located on the incubator cabinet floor or other surface that provides access to at least some of those locations the robotic arm cannot reach.

[0099] In some embodiments, the incubator cabinet is designed to be used in conjunction with an external assay or laboratory automation system. For example, in some embodiments, the incubator cabinet may have a door with an opening large enough to allow the gripper arm to pivot outside the incubator cabinet with sufficient reach for fingers to transport culture vessels or other containers or components between the transport lines of the laboratory automation system and the incubator cabinet or external assay components of the incubator cabinet.

[0100] In some embodiments, the robotic arm is designed, among other things, to transport culture vessels, where the movements of the robotic arm are controlled to prevent sudden movements or accelerations of such vessels or other movements that may cause sample spillage from the vessels. In some embodiments, the robotic arm is designed, among other things, to transport culture vessels, where the movements of the robotic arm are controlled to prevent movements of such vessels that may cause newly seeded cells to clump / concentrate within a particular area of ​​the culture vessel.

[0101] In some embodiments, because the robotic arm transports receptacles or other containers between specific locations within the incubator cabinet, the robotic arm or other components of the incubator can be designed to precisely track where the receptacle or other container is located. In some cases, there are likely to be areas within the incubator cabinet where the robotic arm may be used where other components of the incubator cabinet or walls of the incubator cabinet are located, and therefore where some movement of the robotic arm may be limited. In these cases, a home mechanism can be used for each of the arm's various motors (e.g., x-motor, theta-motor, and z-motor) to properly position the robotic arm at a known location after powering up or before resuming operation if the robotic arm collides with another object.

[0102] In some embodiments, an uninterruptible power supply (“UPS”) is attached to or contained within the incubator cabinet, allowing for orderly shutdown of incubator operations, including preservation of various automation and sample information and completion of any ongoing transport or transfer process (e.g., transport of a container or vessel being conveyed to its destination by a robotic arm). An operator may be alerted to unauthorized opening of the incubator by an audible signal, a visual signal, an electronic signal (e.g., email or text message), or in some other manner. In some embodiments, a sensor or other feature is provided to detect when one or more doors of the incubator are opened (e.g., when an incubator cabinet door, such as an exterior or interior door, is opened). Such a feature is useful because it allows an operator to track or be alerted to any unscheduled or unauthorized opening of the incubator (e.g., incubator cabinet) that could threaten sterility, spoil product, compromise an assay or experiment, etc. In some embodiments, a radio frequency beacon or other signal source is located within an incubator (e.g., incubator cabinet) that can be used to determine the location of one or more devices within the incubator cabinet (e.g., a device having a sensor that can detect the signal and use it to determine its location). In some embodiments, a device may have a signal source and the sensor may be located within one or more of the chambers of the incubator cabinet (e.g., located on the interior surface of an interior chamber).

[0103] In some embodiments, optical signals or lasers (e.g., a grid of laser signals) can be used to determine the location of one or more devices or components within the incubator cabinet. Such information can be communicated, for example, by wire or wirelessly, to an external computer or monitoring station. The information can be used to control the operation of a transfer device, e.g., a robotic arm, within the incubator cabinet to ensure that the transfer device can properly grasp, manipulate, or maneuver a device or item within the incubator cabinet.

[0104] In some embodiments, before a container or vessel is delivered into the incubator cabinet, a user can select an automated system protocol based on the particular container, vessel, ingredient, or cell being inserted into the incubator cabinet. Relevant information related to the incubator and / or one or more incubator components and the cells being grown can be entered into the data system. For example, one or more identifiers, such as barcodes (e.g., 1D or 2D barcodes), can be placed on the container or vessel, and other significant information, such as the type of container, the contents of the container, the assay or operation to be performed on the sample in the container, etc., can be specified. In some embodiments, information related to the incubator system and / or the cells can be contained within one or more barcodes or a combination thereof on a separate data system. The user may also enter information identifying the dimensions (e.g., height, diameter) of the vessel or other container, or the system itself can determine the height scale of the vessel or other container. Using this information, the robotic arm may be requested to transport a particular container, such as when the analytical module is ready to perform an assay or other operation on cells grown in the container, or when the performance of the assay or operation is complete.

[0105] The incubators provided herein include several components, including sensors, environmental control systems, robots, etc., which may operate together under the direction of a computer, processor, microcontroller, or other controller. The components may include, for example, transfer devices (e.g., robotic arms), liquid handling devices, delivery systems for delivering culture vessels, other components to or from the incubator cabinet, environmental control systems for controlling the temperature and other environmental aspects of the incubator cabinet, door operation systems, imaging or detection systems, and cell culture assay systems.

[0106] In some cases, operations such as controlling the operation of the cell culture incubator and / or components provided therein or interfaced therewith may be implemented using hardware, software, or a combination thereof. When implemented in software, the software code can be executed on any suitable processor or collection of processors, whether provided in a single component or distributed among multiple components. Such a processor may be implemented as an integrated circuit, with one or more processors within an integrated circuit component. A processor may be implemented using circuitry in any suitable form.

[0107] In some embodiments, a component (e.g., a controller) controls various processes performed inside the incubator. For example, the controller may direct control devices (e.g., manipulators, imagers, fluid handling systems, etc.). In some embodiments, the controller controls imaging of the cell culture, cell picking, cell thinning (e.g., removal of cell clumps), monitoring cell culture conditions, adjusting cell culture conditions, tracking cell culture vessel movement within the incubator, and / or scheduling of any of the aforementioned processes. Cell Assay

[0108] In certain embodiments, the incubators provided herein are configured to allow one or more assays to be performed in the incubator cabinet or in a chamber operably connected to the incubator cabinet, for example, a separate assay chamber that is part of the incubator. In some embodiments, the incubators provided herein are configured to allow the performance of a cell counting assay, a replicative labeling assay, a cell membrane integrity assay, a cellular ATP-based viability assay, a mitochondrial reductase activity assay, a caspase activity assay, an Annexin V staining assay, a DNA content assay, a DNA degradation assay, a nuclear fragmentation assay, or a combination thereof. Other exemplary assays include BrdU, EdU, or H3-thymidine incorporation assays; DNA content assays using nucleic acid stains such as Hoechst stain, DAPI, actinomycin D, 7-aminoactinomycin D, or propidium iodide; cell metabolism assays such as AlamarBlue, MTT, XTT, and CellTitre Glo; a nuclear fragmentation assay; a cytoplasmic histone-associated DNA fragmentation assay; a PARP cleavage assay; and a TUNEL staining assay.

[0109] In some embodiments, the incubators provided herein are configured to enable digital identification and marking of cells. For example, a cell or multiple cells may be cultured in an incubator described herein and imaged via fluorescence microscopy to digitally mark a cell of interest (e.g., a cell positive for fluorescence) or multiple cells (e.g., a cell population) (e.g., via a computer with imaging software coupled to the incubator). The location of the marked cells may be stored in the computer's memory and accessed at a later time. Digital marking of a cell population may allow the marked cells to be subsequently viewed or manipulated. Subsequent viewing and / or manipulation may be performed at the same location (e.g., the imaging location) where the cells were digitally marked or at a location remote from where the cells were digitally marked (e.g., a manipulation location other than the imaging location). In some cases, digital marking of a cell or multiple cells may be facilitated by aligning a cell culture vessel containing the cells to an imager via one or more fiducial marks. In some embodiments, an incubator as described herein comprises multiple workstations (e.g., one, or two, or three, or four, or five, or more workstations), each configured to allow digital identification and marking of cells.

[0110] In certain embodiments, the incubators provided herein are configured to enable high-throughput screening (HTS) within an incubator cabinet. In some embodiments, HTS refers to testing of and including up to 100,000 compounds per day. In some embodiments, screening assays may be performed in multiwell formats, such as 96-well, 384-well, or 1,536-well formats, and can be performed using automated protocols. Such high-throughput assays can screen thousands of different compounds or compositions in a single day. In particular, each well of a microtiter plate can be used to initiate a separate assay for a selected test compound, or multiple wells can contain test samples of a single compound if concentration or incubation time effects are to be observed. Many plates can be assayed per day, and assay screening for up to about 6,000, 20,000, 50,000, or more than 100,000 different compounds is possible using the assay. Typically, HTS implementation of the assays disclosed herein involves the use of automation. In some embodiments, an integrated robotic system, including one or more robotic arms, transports assay microplates between multiple assay stations for compound, cell, and / or reagent addition, mixing, incubation, and finally, reading or detection. In some aspects, HTS assays may involve preparing, incubating, and analyzing many plates simultaneously, further accelerating the data collection process.

[0111] In some embodiments, assays can include test cells, control cells, and one or more test compounds, e.g., 10, 100, 1000, 10,000, or more test compounds. The cells and test agents can be arranged in one or more containers in a manner suitable for assessing the effect of the test compound on the cells. These assays can be performed in one or more incubator cabinets of one or more incubators described herein. Typically, the containers contain suitable tissue culture medium, and the test compound is present in the tissue culture medium and can be delivered to the culture medium in an automated manner in the incubator cabinet of the incubator provided herein. A medium appropriate for culturing a particular cell type can be selected for use. In some embodiments, the medium is free or essentially free of serum or tissue extracts, while in other embodiments, such components are present. In some embodiments, the cells are cultured on a plastic or glass surface.

[0112] In some embodiments, the techniques described herein may be employed within an automated cell counter. The automated cell counter may be constructed as a device configured to receive a container containing cells and count the number of cells within the container. The automated cell counter may be implemented as a stand-alone device or may be integrated within another device (such as a cell culture incubator). An example of such an automated cell counter is shown in FIG. 5 by automated cell counter 500. As shown, the automated cell counter includes a container mount 510 configured to receive cells within a container (e.g., suspended within a fluid within the container). The container mount 510 may hold the container in a fixed position (e.g., hold the container at an imaging location) for imaging by an imaging system 508. The imaging system 508 may be similar to (or identical to) the imaging system 410 described above with reference to FIG. 4. For example, the imaging system 508 may be configured to capture images of the cells within the container in multiple focal planes. The controller 506 may be coupled to the imaging system 508 and configured to instruct the imaging system 508 to capture images of the containers in the container mount 510. The controller 506 may be configured to analyze the images of the containers captured by the imaging system 508 by performing one or more acts of the processes described above and counting the number of cells in the containers. The controller 506 may display the resulting number regarding the number of cells in the containers via a display 504 coupled to the controller 506. The display 504 may be implemented as, for example, a liquid crystal display (LCD), a plasma display, and / or an organic light-emitting diode (OLED) display. It should be understood that the display 504 may be implemented as a touchscreen display, enabling the controller 506 to receive commands entered from an operator. For example, the controller 506 may receive a command from an operator of the automated cell counter 500 via the display 504 to initiate a cell counting process.

[0113] In some embodiments, one or more components of automated cell counter 500 may be integrated into enclosure 502. For example, imaging systems 508 and 506 may be at least partially enclosed within enclosure 502. Additionally (or alternatively), display 504 and / or vessel mount 510 may be integrated into a sidewall of enclosure 502, allowing an operator to access display 504 and / or vessel mount 510.

[0114] In some embodiments, the imaging systems described above (e.g., imaging system 410 and imaging system 508) may include an optical filter to enhance the contrast between live and dead cells in captured images of the container. Dead cells may thereby be more easily distinguished from live cells. An exemplary implementation of an imaging system including an optical filter is shown in FIG. 6A by imaging system 600A. Imaging system 600A may be configured to capture bright-field images of cells in container 606. As shown, imaging system 600A includes a light source 602, an optical filter 604, and an imaging device 608. Imaging device 608 may be configured to detect light passing through container 606 and capture images of the cells in container 606. Light source 602 may be configured to emit broad-spectrum light (such as white light) and illuminate container 606. Light source 602 may be implemented using light-emitting diodes (LEDs), incandescent lamps, and / or halogen lamps. Optical filter 604 may be configured to filter at least a portion of the light from light source 602. For example, light filter 604 may reduce the intensity of at least some light within a specified range of wavelengths. The particular range of wavelengths of light that light filter 604 is configured to filter may depend, for example, on the type of cells being imaged, the configuration of imaging device 608, the spectrum of light emitted by light source 602, the location of light filter 604, and / or the presence of an agent in container 606 configured to selectively label dead cells. In one illustrative implementation, light source 602 may be a broad-spectrum light source, imaging device 608 may be a monochrome imaging device, and cells in container 606 may be exposed to trypan blue. In this implementation, light filter 604 may be positioned between light source 602 and container 606 and configured to filter light from about 510 nanometers (nm) to about 650 nm (e.g., reduce the light intensity between 510 nm and 650 nm and / or completely block light between 510 nm and 650 nm).

[0115] It should be understood that various modifications can be made to imaging system 600A without departing from the scope of the present disclosure. For example, optical filter 604 may be placed between container 606 and imaging device 608, as shown in FIG. 6B by imaging system 600B, instead of between light source 602 and container 606. Furthermore, imaging systems 600A and / or 600B may include additional elements that change the characteristics of the light. For example, imaging systems 600A and / or 600B may include one or more optical elements for magnifying cells in container 606.

[0116] In some embodiments, imaging system 600A and / or 600B may enhance the contrast between live and dead cells in the captured image of the container without using optical filter 604. For example, light source 602 may be a narrow-spectrum light source (e.g., a light source emitting light with a spectrum that is less than 350 nm in size, less than 300 nm in size, less than 250 nm in size, less than 200 nm in size, less than 150 nm in size, less than 100 nm in size, and / or less than 50 nm in size) configured to emit light with a similar spectrum as broad-spectrum light passing through optical filter 604. For example, light source 602 may be implemented as a yellow light-emitting diode (LED) configured to emit yellow light as an alternative to implementing light source 602 as a white LED configured to emit white light and filter the white light using filter 604 to produce yellow light. Thereby, the same contrast enhancement may be achieved without using optical filter 604. It should be understood that narrow-spectrum light can be generated by any of a variety of light sources, such as colored LEDs (e.g., yellow LEDs, blue LEDs, green LEDs, red LEDs, etc.) and colored lasers (e.g., yellow lasers, blue lasers, green lasers, red lasers). In some embodiments, the yellow LED or yellow laser emits light within a wavelength range of 570 nm to 590 nm. In some embodiments, the blue LED or blue laser emits light within a wavelength range of 450 nm to 500 nm. In some embodiments, the green LED or green laser emits light within a wavelength range of 500 nm to 570 nm. In some embodiments, the red LED or red laser emits light within a wavelength range of 610 nm to 760 nm.

[0117] The controllers described above (e.g., controllers 412 and 506) may be implemented in any of a variety of ways. An exemplary implementation of a controller is shown in FIG. 7 by controller 700. As shown, controller 700 may include one or more computer hardware processors 702 and one or more articles of manufacture including non-transitory computer-readable storage media (e.g., memory 704 and one or more non-volatile storage devices 706). Processor 702 may control writing and reading data to and from memory 704 and non-volatile storage device 706 in any suitable manner. To perform any of the functionality described herein, processor 702 may execute one or more processor-executable instructions stored in one or more non-transitory computer-readable storage media (e.g., memory 704), which may serve as non-transitory computer-readable storage media storing processor-executable instructions for execution by processor 702.

[0118] It should be understood that various modifications may be made to the controller 700 without departing from the scope of this document. In some embodiments, one or more components of the controller 700 shown in FIG. 7 may be separate from the controller 700 or may be communicatively coupled to the controller 700. For example, the memory 704 and / or one or more non-volatile storage devices 706 may be separate from the controller 700.

[0119] The terms "program" or "software" are used herein in a generic sense to refer to any type of computer code or set of processor-executable instructions that can be employed to program a computer or other processor and implement various aspects of the embodiments as discussed above. Additionally, according to one aspect, one or more computer programs that, when executed, perform the methods of the disclosure provided herein need not reside on a single computer or processor, but may be distributed in a modular manner among different computers or processors to implement various aspects of the disclosure provided herein.

[0120] Processor-executable instructions may be in many forms, such as program modules, executed by one or more controllers or other devices. Generally, program modules include routines, programs, objects, components, data structures, etc. that perform particular tasks or implement particular abstract data types. Typically, the functionality of the program modules may be combined or distributed as desired in various embodiments.

[0121] As used herein and in the claims, the phrase "at least one" in reference to a list of one or more elements should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but does not necessarily include at least one of every element specifically set forth in the list of elements, nor does it exclude any combination of elements in the list of elements. This definition also allows for the optional presence of elements other than those specifically identified in the list of elements to which the phrase "at least one" refers, whether related or unrelated to those elements specifically identified. Thus, for example, "at least one of A and B" (or, equivalently, "at least one of A or B" or, equivalently, "at least one of A and / or B") can refer in one embodiment to at least one A (optionally including more than one element other than B), with no B present; in another embodiment to at least one B (optionally including elements other than A), with no A present, with more than one element other than A; in yet another embodiment to at least one A, with more than one element other than A, and at least one B, with more than one element other than A, with other elements present; etc.

[0122] As used in this specification and the claims, the term "and / or" should be understood to mean "either or both" of the elements so conjoined, i.e., elements that are present conjunctively in some cases and disjunctively in other cases. Multiple elements listed with "and / or," i.e., "one or more" of the elements so conjoined, should be construed in the same manner. Other elements, whether related or unrelated to those specifically identified elements, may optionally be present other than the elements specifically identified by the "and / or" clause. Thus, as a non-limiting example, a reference to "A and / or B," when used in conjunction with open-ended language such as "comprising," can refer in one embodiment to A only (optionally including elements other than B); in another embodiment to B only (optionally including elements other than A); in yet another embodiment to both A and B (optionally including other elements); etc.

[0123] The use of ordinal terms such as "first," "second," "third," etc. in the claims to modify claim elements does not, in itself, indicate any priority, precedence, or ordering of one claim element prior to another, or the chronological order in which method actions are performed. Such terms are used merely as labels to distinguish one claim element having a certain name from another element having the same name (in the absence of the use of ordinal terms). The phraseology and terminology used herein are for purposes of description and should not be regarded as limiting. The use of "comprises," "has," "contains," "involves," and variations thereof is intended to encompass the items listed thereafter and additional items.

[0124] The terms "approximately" and "about" may be used to mean, in some embodiments, within ±20% of a target dimension, in some embodiments, within ±10% of a target dimension, in some embodiments, within ±5% of a target dimension, and even in some embodiments, within ±2% of a target dimension. The terms "approximately" and "about" may include the target dimension.

[0125] Having described in detail several embodiments of the techniques described herein, various modifications and improvements will readily occur to those skilled in the art. Such modifications and improvements are intended to be within the spirit and scope of the present disclosure. Accordingly, the foregoing description is by way of example only and is not intended to be limiting. The techniques are limited only as defined by the following claims and equivalents thereof. The present invention also provides the following items. (Item 1) 1. A system comprising: an imaging system configured to image a plurality of cells in a container in a plurality of focal planes; at least one controller coupled to the imaging system, When executed, controlling the imaging system to capture a plurality of images of at least some of the cells, each of the plurality of images being captured within a respective focal plane of the plurality of focal planes; determining an area of ​​at least one cell from the at least some cells in each of the plurality of images; selecting an image from the plurality of images as a focused image using an area of ​​the at least one cell in at least some of the plurality of images; estimating the number of cells in the focused image; at least one controller coupled to a memory containing instructions; A system comprising: (Item 2) 2. The system of claim 1, wherein the plurality of cells are exposed to a chemical that selectively labels dead cells. (Item 3) Item 3. The system of item 2, wherein the agent includes a dye that selectively stains the dead cells, and the imaging system includes an optical filter configured to filter at least some visible light. (Item 4) 4. The system of claim 3, wherein the imaging system comprises a monochrome imaging device and a light source configured to emit visible light, and the filter is disposed between the light source and the monochrome imaging device. (Item 5) Item 4. The system of item 3, wherein the filter is configured to filter at least some visible light with wavelengths greater than 510 nanometers (nm). (Item 6) Item 4. The system of item 3, wherein the filter is configured to filter at least some visible light with wavelengths below 650 nanometers (nm). (Item 7) 7. The system of claim 5 or 6, wherein the dye comprises trypan blue. (Item 8) Item 10. The system of item 1, wherein the one image from the plurality of images is selected as the focused image at least in part by using an image from the plurality of images with the smallest area of ​​the at least one cell. (Item 9) Item 10. The system of item 1, wherein the area of ​​the at least one cell is identified, at least in part, by counting the number of pixels associated with the at least one cell. (Item 10) Item 10. The system of item 1, wherein the area of ​​the at least one cell is identified, at least in part, by estimating an axial length of the at least one cell. (Item 11) estimating the number of cells in the focused image includes: identifying a plurality of objects within the focused image; classifying a first subset of the plurality of objects as living cells; counting the number of viable cells in a first subset of the plurality of objects; Item 1. The system according to item 1, comprising: (Item 12) estimating the number of cells in the focused image includes: classifying a second subset of the plurality of objects as dead cells; counting the number of dead cells in a second subset of the plurality of objects; Item 12. The system according to item 11, comprising: (Item 13) Item 12. The system of item 11, wherein identifying the plurality of objects includes separating a foreground of the focused image from a background of the focused image and identifying at least one portion within the foreground of the focused image as an object. (Item 14) Item 14. The system of item 13, wherein separating the foreground of the focused image from the background of the focused image includes thresholding the focused image. (Item 15) Item 12. The system of item 11, wherein estimating the number of cells in the focused image includes classifying a second subset of the plurality of objects as debris. (Item 16) Classifying a first subset of the plurality of objects as live cells includes: classifying a first object from a first subset of the plurality of objects as a single living cell; classifying a second object from the first subset of the plurality of objects as a living cell mass; estimating a number of viable cells within the second object based, at least in part, on an intensity contour associated with the second object; and Item 12. The system according to item 11, comprising: (Item 17) Item 17. The system of item 16, wherein classifying the first object from a first subset of the plurality of objects as the single living cell comprises providing input to a classifier selected from the group consisting of a decision tree, a neural network, a discriminant function, a Bayesian network, and a support vector machine. (Item 18) Item 17. The system of item 16, wherein classifying the second object from the first subset of the plurality of objects as the living cell mass comprises providing input to a classifier selected from the group consisting of a decision tree, a neural network, a discriminant function, a Bayesian network, and a support vector machine. (Item 19) Item 10. The system of claim 1, further comprising a container, the container being a hemocytometer. (Item 20) Item 1, wherein the imaging system comprises at least one imaging device selected from the group consisting of a monochrome imaging device, a red / green / blue (RGB) imaging device, a spectral imaging device, a fluorescence imaging device, and a multi-channel imaging device. (Item 21) Item 10. The system of item 1, wherein the plurality of images includes at least one bright field image. (Item 22) 1. A method comprising: receiving a plurality of cells in a container; capturing focused images of at least some cells within the plurality of cells, wherein capturing the focused images includes: capturing a plurality of images of the at least some cells using the imaging system, each of the plurality of images being captured within a respective one of a plurality of focal planes; determining, using at least one controller, an area of ​​at least one cell from the at least some cells in each of the plurality of images; selecting, using the at least one controller, an image from the plurality of images as the focused image using an area of ​​the at least one cell in at least some of the plurality of images; estimating a number of cells in the focused image using the at least one controller; A method comprising: (Item 23) estimating the number of cells in the focused image includes: identifying a plurality of objects within the focused image; classifying a first subset of the plurality of objects as living cells; counting the number of viable cells in a first subset of the plurality of objects; Item 23. The method according to Item 22, comprising: (Item 24) identifying the plurality of objects Separating the foreground of the focused image from the background of the focused image; identifying at least one portion in a foreground of the focused image as an object; Item 24. The method according to Item 23, comprising: (Item 25) 24. The method of claim 23, wherein estimating the cell count within the at least some cells comprises classifying a second subset of the plurality of objects as debris. (Item 26) Classifying a first subset of the plurality of objects as live cells includes: classifying a first object from a first subset of the plurality of objects as a single living cell; classifying a second object from the first subset of the plurality of objects as a living cell mass; estimating the number of viable cells within the second object based at least in part on an intensity contour associated with the second object; and Item 24. The method according to Item 23, comprising: (Item 27) 1. An automated cell counter comprising: a container mount configured to receive a container containing a plurality of cells; an imaging system configured to image the plurality of cells in a plurality of focal planes; at least one controller coupled to the imaging system; When executed, controlling the imaging system to capture a plurality of images of at least some of the cells; determining an area of ​​at least one cell from the at least some cells in each of the plurality of images; selecting an image from the plurality of images as the focused image using an area of ​​the at least one cell in at least some of the plurality of images; estimating the number of cells in the focused image; at least one controller coupled to a memory containing instructions; An automated cell counter comprising: (Item 28) estimating the number of cells in the focused image includes: identifying a plurality of objects within the focused image; classifying a first subset of the plurality of objects as viable cells; counting the number of viable cells in a first subset of the plurality of objects; 28. The automated cell counter according to Item 27, comprising: (Item 29) estimating the number of cells in the focused image includes: classifying a second subset of the plurality of objects as dead cells; counting the number of dead cells in a second subset of the plurality of objects; Item 29. The automated cell counter according to Item 28, comprising: (Item 30) 1. A system comprising: an imaging system configured to image the plurality of cells in the container; at least one controller coupled to the imaging system; When executed, controlling the imaging system to capture a plurality of focused images of at least some cells within the plurality of cells; At least in part, Identifying a plurality of objects within the focused image; classifying a subset of the plurality of objects as cells; counting the number of cells in a subset of the plurality of objects classified as cells; and estimating the number of cells in the focused image by at least one controller coupled to a memory containing instructions; A system comprising: (Item 31) 31. The system of claim 30, wherein classifying a subset of the plurality of objects as cells comprises classifying a subset of the plurality of objects as viable cells. (Item 32) 32. The system of claim 31, wherein counting the number of cells in a subset of the plurality of objects classified as cells comprises counting the number of viable cells in the subset of the plurality of objects. (Item 33) 1. A cell culture incubator comprising: an incubator cabinet configured to receive a container for storing a plurality of cells; an imaging system configured to image the plurality of cells; at least one controller coupled to the imaging system; When executed, controlling the imaging system to capture a plurality of images of at least some of the cells; determining an area of ​​at least one cell from the at least some cells in each of the plurality of images; selecting an image from the plurality of images as the focused image using an area of ​​the at least one cell in at least one of the plurality of images; estimating the number of cells in the focused image; at least one controller coupled to a memory containing instructions; a cell culture incubator comprising: (Item 34) 34. The cell culture incubator of item 33, further comprising a storage location within the interior chamber of the incubator cabinet for storing the container. (Item 35) 35. The cell culture incubator of claim 34, further comprising a container transfer device configured to move the container from the storage location to an imaging location of the imaging system or from the imaging location to the storage location. (Item 36) estimating the number of cells in the focused image includes: identifying a plurality of objects within the focused image; classifying the first subset of the plurality of objects as viable cells; counting the number of viable cells in a first subset of the plurality of objects; 34. The cell culture incubator according to item 33, comprising: (Item 37) estimating the number of cells in the focused image includes: classifying a second subset of the plurality of objects as dead cells; counting the number of dead cells in a second subset of the plurality of objects; 37. The cell culture incubator according to item 36, comprising:

Claims

1. 1. A system comprising: an imaging system configured to generate bright field images of a plurality of cells in the container within a plurality of focal planes; at least one controller coupled to the imaging system, When executed, controlling the imaging system to capture a plurality of Z-stack brightfield images of at least some of the cells to enable capture of a focused image of each of the at least some of the cells, wherein each of the plurality of Z-stack brightfield images comprises two-dimensional x-y images at different focal lengths corresponding to focal planes at different z-coordinates relative to the imaging system; determining an area of ​​at least one cell in each of the Z-stack bright field images by separating a foreground of the image from a background of the image, generating a binary mask indicating for each pixel whether it is the foreground or background, identifying objects in the foreground having a size of at least one cell, and identifying objects having a size greater than the size of a cell as cell clusters, wherein the pixels in the foreground correspond to focused images of cells; For each object determined to be a cell mass, finding at least one sharp peak in the intensity contour in the object image that corresponds to the center of the cell; counting the number of objects identified as single cells in all of the plurality of Z-stack bright-field images, and counting the number of peaks within the objects identified as cell clusters in all of the plurality of Z-stack bright-field images; at least one controller coupled to a memory containing instructions; A system comprising:

2. The system of claim 1 , wherein the plurality of cells are exposed to a chemical that selectively marks dead cells.

3. The system of claim 2 , wherein the agent comprises a dye that selectively stains the dead cells, and the imaging system comprises an optical filter configured to filter at least some visible light.

4. The system of claim 3 , wherein the bright field imaging system comprises a monochrome imaging device and a light source configured to emit visible light, the filter being disposed between the light source and the monochrome imaging device.

5. The system of claim 3 , wherein the filter is configured to filter at least some visible light with wavelengths greater than 510 nanometers (nm).

6. The system of claim 3 , wherein the filter is configured to filter at least some visible light with wavelengths below 650 nanometers (nm).

7. The system of claim 5 , wherein the dye comprises trypan blue.

8. The system of claim 1 , wherein the area of ​​the at least one cell is identified by counting the number of pixels associated with the at least one cell.

9. The system of claim 8 , wherein the area of ​​the at least one cell is identified by estimating an axial length of the at least one cell.

10. estimating the number of cells in the focused image identifying a plurality of objects within the focused image; classifying a first subset of the plurality of objects as living cells; counting the number of viable cells in the first subset of the plurality of objects; The system of claim 1 , comprising:

11. estimating the number of cells in the focused image includes: classifying a second subset of the plurality of objects as dead cells; counting the number of dead cells in the second subset of the plurality of objects; The system of claim 10, comprising:

12. The system of claim 1 , further comprising, after generating the mask, reclassifying artifacts in the foreground as part of the background and / or reclassifying artifacts in the background as part of the foreground.

13. The system of claim 1 , wherein separating the foreground of the Z-stack brightfield image from the background of the Z-stack brightfield image comprises thresholding the Z-stack brightfield image.

14. The system of claim 10 , wherein estimating the number of cells in the focused image includes classifying a second subset of the plurality of objects as debris.

15. Classifying the first subset of the plurality of objects as living cells comprises: classifying a first object from the first subset of the plurality of objects as a single living cell; classifying a second object from the first subset of the plurality of objects as a living cell mass; estimating the number of viable cells within the second object based on an intensity contour associated with the second object; and The system of claim 10, comprising:

16. 1. A method comprising: receiving a plurality of cells in a container; capturing a focused bright field image of at least some cells within the plurality of cells, wherein capturing the focused image includes: capturing a plurality of Z-stack brightfield images of the at least some cells using the imaging system to capture a focused image of each of the at least some cells, wherein each of the plurality of Z-stack brightfield images comprises two-dimensional x-y images at different focal lengths corresponding to focal planes at different z-coordinates relative to the imaging system; determining an area of ​​at least one cell in each of the Z-stack bright field images by using at least one controller to separate a foreground of the image from a background of the image, generate a binary mask indicating for each pixel whether it is the foreground or background, identify objects in the foreground having a size of at least one cell, and identify objects having a size larger than the size of a cell as cell clusters, wherein the pixels in the foreground correspond to focused images of cells; For each object determined to be a cell mass, finding at least one sharp peak in the intensity contour in the object image that corresponds to the center of the cell; counting the number of objects identified as single cells in all of the plurality of Z-stack bright-field images; and counting the number of peaks within the objects identified as cell clusters in all of the plurality of Z-stack bright-field images. , counting the number of cells, and A method comprising:

17. estimating the number of cells in the focused image includes: identifying a plurality of objects within the focused image; classifying a first subset of the plurality of objects as living cells; counting the number of viable cells in the first subset of the plurality of objects; 17. The method of claim 16, comprising:

18. identifying the plurality of objects Separating the foreground of the focused image from the background of the focused image; identifying at least one portion in the foreground of the focused image as an object; 18. The method of claim 17, comprising:

19. 18. The method of claim 17, wherein estimating the cell count within the at least some cells comprises classifying a second subset of the plurality of objects as debris.

20. Classifying the first subset of the plurality of objects as living cells comprises: classifying a first object from the first subset of the plurality of objects as a single living cell; classifying a second object from the first subset of the plurality of objects as a living cell mass; estimating the number of viable cells within the second object based on an intensity contour associated with the second object; and 18. The method of claim 17, comprising:

Images