JP2014018184A - Method for evaluating pluripotent stem cells by image analysis - Google Patents

Abstract

PROBLEM TO BE SOLVED: To provide a method for easily evaluating a differentiation state of pluripotent stem cells, i.e., quality of the cells, without depending on a determination of experienced technicians and to provide a method for automatically determining the pluripotent stem cells that start differentiation.SOLUTION: A method for evaluating quality of the pluripotent stem cells is provided, the method applying a differential filter to images of colony that is formed by the pluripotent stem cells, then evaluating the quality of the pluripotent stem cells on the basis of an obtained differential images.

Description

  The present invention relates to a method for evaluating the quality of pluripotent stem cells by performing image processing on colony images of pluripotent stem cells. The present invention also relates to a method for automatically determining the quality of a pluripotent stem cell colony by processing an image of a pluripotent stem cell colony.

  Pluripotent stem cells are widely used in various fields such as tissue differentiation research, drug testing and regenerative medicine because of their differentiation pluripotency capable of differentiating into any tissue. In particular, since the establishment of iPS cells, research in this field has been remarkably developed, and various efforts for realizing regenerative medicine have been made all over the world.

  By the way, pluripotent stem cells are easy to differentiate, and once differentiated, there is a possibility of losing pluripotency. Therefore, pluripotent stem cells are cultured while maintaining the undifferentiated state of pluripotent stem cells. Therefore, maintaining an undifferentiated state is one of the most important factors in culturing pluripotent stem cells.

  In order to maintain an undifferentiated state, use of a drug that inhibits differentiation, removal of pluripotent stem cells that have started differentiation, and the like are performed. In the large-scale preparation of pluripotent stem cells, one of the most problematic problems is the removal of pluripotent stem cells that have started to differentiate. If removal of cells that have started differentiation is insufficient, it may induce the differentiation of surrounding cells and adversely affect the entire cultured cell. However, the differentiation state of pluripotent stem cells is determined by skilled technicians. This is because it is difficult to make a judgment if you do not follow. For this reason, there is a limit to the large-scale preparation of pluripotent stem cells.

  Therefore, development of a method for confirming the differentiation state of pluripotent stem cells without depending on at least judgment of a skilled engineer and development of a method capable of automatically determining pluripotent stem cells that have started differentiation have been desired. In this regard, a method for detecting loss of pluripotency of stem cells using an odor sensor (Patent Document 1) has been developed. However, a complicated and large-scale apparatus is required, and development of a simple method is still desired. ing.

JP 2010-246441 A

  An object of the present invention is to provide a method for simply evaluating the differentiation state of a pluripotent stem cell, that is, the quality, regardless of judgment of a skilled engineer. Another object of the present invention is to provide a method for automatically determining the quality of a pluripotent stem cell (hereinafter sometimes simply referred to as “determination”).

  The present inventors form undifferentiated good pluripotent stem cells based on images obtained by performing differential filter processing on microscopic images of colonies formed by pluripotent stem cells during adhesion culture. It was found that colonies formed by defective pluripotent cells that have started to differentiate from colonies can be distinguished. The present invention is based on such knowledge.

That is, according to the present invention, the following inventions are provided.
(1) A method for evaluating the quality of a pluripotent stem cell colony based on a differential filtering image (differential image) of a colony image formed by a pluripotent stem cell.
(2) The method according to (1), wherein the quality of the colony is evaluated based on an image pattern obtained from a differential image of pluripotent stem cells.
(3) The differential image is digitized for each pixel according to the gradation of each pixel, and then the quality of the colony is evaluated based on the numerical value of the central part of the colony and, in some cases, the numerical value of the peripheral part. The method according to (1).
(4) The method according to (1), wherein the differential image is digitized for each pixel according to the gradation of each pixel, and then the quality of the colony is evaluated based on the obtained numerical distribution.
(5) From the differential image, digitization is performed for each pixel in accordance with the gradation of each pixel, and then at least one type of fit function created in advance for the numerical distribution of colonies is calculated for the numerical distribution of colonies to be evaluated. The method according to (4) above, wherein the quality of the colony is evaluated by curve fitting.
(6) The fitting function created in advance is
A fitting function (f _good function) representing a convex shape, and / or
A fit function (f _bad function) that represents a concave shape at the center of the colony and a convex shape at the periphery.
(However, the position of the straight line passing through the colony center is the horizontal axis (X axis) of the plane orthogonal coordinate system, and the numerical distribution (Y axis) is the vertical axis. The method according to (5) above, which creates a graph.
(7) The method according to (6) above, wherein the fitting function created in advance is at least two types of fitting functions including an f _good function and an f _bad function.
(8) The f _bad function is
(Condition B1) Converge in the limits of x → −∞ and x → ∞,
(Condition B2) Within a colony, it becomes 0 or more for any real number x, and
(Condition B3) The method according to (6) or (7) above, wherein any one, two or all conditions selected from having one minimum value and two maximum values in a colony are satisfied.
(9) The f _bad function is
,
,
,and,
The method according to any one of (6) to (8), wherein the method is selected from the group consisting of:
(10) The f _bad function is
The method according to (9), wherein
(11) The f _good function is
(Condition G1) Converge in the limits of x → −∞ and x → ∞.
(Condition G2) 0 or more for any real number x in the colony, and (Condition G3) One, two or all conditions selected from having one local maximum in the colony The method according to any one of (6) to (10) above.
(12) The f _good function is
,
,and,
The method according to any one of (6) to (11), wherein the method is selected from the group consisting of:
(13) The f _good function is
The method according to (12), wherein
(14) Any one of the above (6) to (13), in which the quality of the colony is evaluated using as an index the degree of deviation between at least one approximate curve obtained by curve fitting and the numerical distribution of the colony to be evaluated The method of crab.
(15) The method according to any one of (6) to (14) above, wherein the quality of the colony is evaluated using a parameter extracted from at least one kind of approximate curve obtained by curve fitting as an index.
(16) parameter, 1 in the _colony, the maximum value of _{f good function,} the maximum value of _{f bad function,} the minimum value of _{f bad} function, is selected from the group consisting of the minimum value of the maximum value and the actual measured values for The method according to (15) above, which is the above parameter.
(17) The method according to (15) or (16) above, comprising evaluating the quality of the colony using the sum, difference, product or ratio of the two parameters as an index.
(18) Index of the sum, difference, product or ratio of the sum, difference, product or ratio of two parameters and the sum, difference, product or ratio of two parameters in another two parameter combination The method as described in said (17) including evaluating the quality of a colony as.
(19) The above parameters (17) or (18), wherein the parameters are two parameters selected from the group consisting of the maximum value of the f _good function, the maximum value of the f _bad function, and the minimum value of the f _bad function in the colony. ) Method.
(20) The following four parameters calculated for each colony from the approximate curve:
Parameter A: difference between the central value of the f _good function and the minimum value of the f _bad function,
Parameter B: difference between the maximum value and the minimum value of the f _bad function,
Parameter C: at least one selected from the group consisting of the maximum value of the actual measurement value and the minimum value of the actual measurement value at the center of the colony, and parameter D: the root mean square of the difference between the f _good function in the colony and the actual measurement value The method according to (18), wherein the quality of the colony is evaluated based on the parameters.
(21) The method according to (20), wherein the evaluation is performed based on a numerical value obtained by weighting and adding two or more parameters selected from the parameters A to D.
(22) A program for causing a computer to execute the method according to any one of (1) to (20).
(23) A computer-readable recording medium on which the program according to (22) is recorded.
(24) A computer in which the program according to (22) is recorded in an internal storage device.
(25) An automatic determination system for the quality of pluripotent stem cell colonies, comprising the computer according to (24).

  The present invention is advantageous in that it does not require manipulation of cells such as staining, and can be evaluated based only on images of pluripotent stem cell colonies. The present invention is further advantageous in that image processing and image analysis can be fully automated.

FIG. 1 is a diagram illustrating a result of applying various differential filters to an image of colonies formed by iPS cells. FIG. 1A shows a Sobel filtered image of an iPS cell colony determined to be undifferentiated (good) by a skilled technician, and FIG. 1B shows that differentiation has started (bad) by a skilled technician. The Sobel filter process image of the iPS cell colony judged is shown. 1C to 1J are Sobel secondary differential filter processed images (FIG. 1C), 5 × 5 Sobel filtered image (FIG. 1D), Prewitt filtered image (FIG. 1E), and gradient filter of iPS cell colonies determined to be defective. Processed image (FIG. 1F), Max-Min filter processed image (FIG. 1G), Roberts filter processed image (FIG. 1H), Robinson operator processed image (FIG. 1I), Kirsch filter processed image (FIG. 1J), Charr operator processed image ( FIG. 1K), a Laplace filtered image (FIG. 1L), and a modified Laplace filtered image (FIG. 1M). In FIG. 1, the image is 40 × 40 pixels after the 20 × 20 pixel averaging process, the background removal process, and the contrast adjustment after the differential filter process. FIG. 2 is a diagram showing an image processing process of an iPS cell colony determined to be undifferentiated (good) by a skilled engineer. 2A shows a phase-contrast microscope image, FIG. 2B shows an image obtained by performing averaging processing of 20 × 20 pixels, background removal processing, and contrast adjustment after Sobel filtering, and FIG. 2D shows an image of a mask obtained from 2B, FIG. 2D shows an image obtained by masking FIG. 2B, FIG. 2E shows an extracted image of an embryoid body part, and FIG. 2F shows a composite of FIG. 2D and FIG. FIG. 2G shows a 40 × 40 matrix obtained by converting FIG. 2F into a numerical value. FIG. 3 is a diagram showing a process of image processing of an iPS cell colony that is determined to have been differentiated (defective) by a skilled engineer. 3A shows a phase-contrast microscope image, FIG. 3B shows an image obtained by performing averaging processing of 20 × 20 pixels, background removal processing, and contrast adjustment after Sobel filter processing, and FIG. Fig. 3D shows an image of the mask obtained from 3B, Fig. 3D shows an image obtained by masking Fig. 3B, Fig. 3E shows an extracted image of an embryoid body part, and Fig. 3F shows a combination of Figs. 3D and 3E. FIG. 3G shows a 40 × 40 matrix obtained by converting FIG. 3F into a numerical value. FIG. 4 is a diagram showing a process of image processing of a colony including an embryoid body part. 4A shows a phase-contrast microscope image, FIG. 4B shows an image obtained by performing averaging processing of 20 × 20 pixels, background removal processing and contrast adjustment after Sobel filter processing, and FIG. 4D shows an image of the mask obtained from 4B, FIG. 4D shows an image obtained by masking FIG. 4B, FIG. 4E shows an extracted image of the embryoid body part, and FIG. 4F shows a combination of FIG. 4D and FIG. FIG. 4G shows a 40 × 40 matrix obtained by converting FIG. 4F into a numerical value. FIG. 5 shows a typical gradation numerical distribution seen in a differential image of an iPS cell colony judged good (FIG. 5A) and a typical gradation numerical distribution seen in an iPS cell colony judged poor. It is a figure which shows (FIG. 5B). 5A and 5B show f _good (x) and f _bad (x) that are curve-fitted to the respective numerical distributions. FIG. 6 is a diagram for explaining the parameters A to D. FIG. 7 is a diagram in which the parameters A to E are compared with the differentiation state of the iPS cell colony. FIG. 8 is a diagram showing the relationship between the recovery rate of good iPS cell colonies and the contamination rate of bad iPS cell colonies when each of parameters A to E is used. That is, FIGS. 8A to E show the recovery rate of good iPS cell colonies on the horizontal axis and the contamination rate of bad iPS cell colonies on the vertical axis.

Detailed Description of the Invention

  In the present invention, pluripotent stem cells can be evaluated for each colony. That is, according to the present invention, pluripotent stem cells can be evaluated by evaluating the differentiation state of pluripotent stem cells for each colony (that is, by evaluating the quality of a colony for each colony). . Here, a good colony is a colony evaluated that does not include cells that have started differentiation (consisting of undifferentiated cells), and a poor colony is evaluated to include cells that have started differentiation. It is a colony.

  The method of the present invention is a method for evaluating the quality of a colony of pluripotent stem cells based on a differential filtered image (differential image) of an image of colonies formed by pluripotent stem cells. According to the present invention, the evaluation of the quality of the pluripotent stem cell colony was obtained by (A) acquiring an image of the pluripotent stem cell colony (acquisition of the image) and (B) step (A). Obtaining a differential image by subjecting the image to differential filter processing (image processing), and evaluating the quality of the pluripotent stem cell colony based on the differential image obtained in step (B) (image analysis) ). Hereinafter, the evaluation method of the present invention will be specifically described by dividing it into a process (A), a process (B) and a process (C).

(A) Acquisition of Colony Image of Pluripotent Stem Cell According to the present invention, an image of a colony formed by a pluripotent stem cell during adhesion culture can be acquired as a microscope image using an optical microscope, for example. . As the optical microscope, a transmission observation type microscope can be used. Preferably, a bright field microscope, a dark field microscope, a phase contrast microscope, a differential interference microscope, and the like can be used. From the viewpoint of observing pluripotent stem cells (particularly iPS cells), a phase contrast microscope is particularly preferably used. The colony image can be taken into a computer or the like using a camera such as a CCD camera or a CMOS camera, and then processed electronically. The colony image has a resolution of 3.2 μm / pixel or less, preferably 1.6 μm / pixel or less, and as long as it has the above-mentioned resolution, it is not necessarily acquired using a microscope.

  The term “pluripotent stem cell” used in the present invention means a cell having the ability to differentiate into cells derived from any of the three germ layers, and is particularly limited as long as it is a pluripotent stem cell that forms a colony by adhesion culture. It can be used without. The pluripotent stem cells used in the present invention are not particularly limited, but can preferably be mammalian pluripotent stem cells such as primate cells and rodent cells, and more preferably humans, monkeys, and mice. Rat, guinea pig, hamster, rabbit, cat, dog, sheep, pig, cow or goat pluripotent stem cell, more preferably human pluripotent stem cell. The pluripotent stem cells used in the present invention include embryonic stem cells (ES cells), inducible pluripotent stem cells (iPS cells or induced pluripotent stem cells), Muse cells (Multilineage-differentiating Stress Enduring Cell), embryonic Examples include pluripotent stem cells such as tumor cells (EC cells) or embryonic germ stem cells (EG cells), preferably ES cells or iPS cells. Accordingly, the pluripotent stem cells used in the present invention are preferably mammalian ES cells or iPS cells, more preferably ES cells or iPS cells such as primates or rodents, and more preferably Human, monkey, mouse, rat, guinea pig, hamster, rabbit, cat, dog, sheep, pig, bovine or goat ES cells or iPS cells, most preferably human ES cells or human iPS cells. According to the present invention, feeder cells may or may not be used.

(B) Image processing of colony of pluripotent stem cells According to the present invention, image processing of a colony of pluripotent stem cells is
(B1) The image of the colony is subjected to differential filter processing to obtain a differential processed image, and in order to improve the accuracy of image analysis of the obtained differential processed image, the following steps (B1-a), ( B1-b) and / or (B1-c)
(B1-a) removing background.
(B1-b) performing pixel averaging processing;
(B1-c) performing contrast adjustment;
It can be performed by attaching to the process. (The obtained image is assumed to be image 1.)

The image 1 obtained in the step (B1) may be subjected to the following steps (B2), (B3) and / or (B4) as necessary from the viewpoint of improvement in analysis accuracy and analysis speed. it can:
(B2) Create a mask (image 2) from the colony image, and mask the image 1 using the created mask (the obtained image after masking is referred to as an image 3),
(B3) Performing image processing to remove the embryoid body part present in the colony on image 1 or 3 (the obtained image after removal is referred to as image 5),
(B4) The resolution of the image 1, 3 or 5 is reduced as necessary (the image with the reduced resolution is referred to as an image 6).
In this specification, the image obtained by the step (B) is referred to as a differential image.

  Hereinafter, each process of a process (B) is demonstrated concretely. Note that all of the image processing described below is, for example, image processing software ImageJ (http://rsbweb.nih.gov/ij/) provided free of charge by the National Institute of Health (NIH). The image processing software can be executed by a computer.

(B1) Image Differential Filter Processing The obtained image can be subjected to image processing using a differential filter. Although the differential filter processing can be performed on a color image, it is preferably performed after conversion to a gray scale image in order to facilitate analysis. The grayscale image is not particularly limited, but may be 1 to 16 bits, preferably 8 to 16 bits, and more preferably 8 bits. As the differential filter, either a primary differential filter or a secondary differential filter may be used. The differential filter can be an n × n matrix (n is a natural number of 2 or more), but preferably, a matrix filter with n of 2, 3, 4, or 5 can be used, and more preferably Can use a 3 × 3 matrix filter. Such a differential filter can be appropriately designed by those skilled in the art. For example, the differential filter is not particularly limited,
3x3 Sobel filter:
5x5 sobel filter:
, Prewitt filter:
, Gradient filter:
, Roberts filter:
The Robinson operator:
Kirsch filter:
A Max-Min filter having a difference between a maximum value and a minimum value within a 3 × 3 pixel surrounding the target pixel as a value of the pixel,
Scharr operator,
Sobel second derivative filter:
And Laplacian filter:
And so on.

A person skilled in the art can also perform filter processing using a differential filter created by modifying these filters. For example, the Laplacian filter is appropriately modified, and the following modified Laplacian filter:
May be created and used as a differential filter.

  The method of differential filtering is well known to those skilled in the art. For example, when using a primary differential filter in the vertical direction and the horizontal direction, the value of each pixel is generally obtained by the primary differential filter. Is obtained as the square root of the sum of squares of the values of.

  After the differential filter processing, (B1-a) background removal processing, (B1-b) pixel averaging processing, and / or (B1-c) contrast adjustment are performed as appropriate for the purpose of improving the accuracy of image analysis. be able to. Pixel averaging processing, background removal processing, and contrast adjustment can be appropriately performed regardless of the order. The obtained image is stored as an analysis image (image 1).

(B1-a) Background Removal Processing Although background removal is an optional step, it is preferably performed in order to increase the accuracy of the subsequent analysis, and is not particularly limited. For example, the Rolling Ball algorithm (Stanley Sternberg, Biomedical Image Processing, IEEE Computer, 1893, January).

(B1-b) Pixel Averaging Processing Pixel averaging is an optional step, and is preferably performed in order to increase the accuracy of the subsequent analysis, and is not particularly limited. An averaging process can be performed by replacing the value of the pixel with an average value of n × n pixels. n can be appropriately set by those skilled in the art. For example, n is 20.

(B1-c) Contrast adjustment Contrast adjustment is a completely arbitrary process, and may or may not be performed. However, when it is performed, any one of differential filter processing and (1a) and (1b) processing is performed. Can be performed after one or more of the following. As a method for adjusting the contrast, a method well known to those skilled in the art can be used. For example, in the case of an 8-bit grayscale image, the maximum gradation value of all pixels can be converted to 255, the minimum value can be converted to 0, and contrast adjustment can be performed so that the entire gradation area can be used effectively. .

  In the present invention, for example, (B1-c) contrast adjustment is performed after differential image processing, then (B1-b) pixel averaging processing is performed, and (B1-c) contrast adjustment is performed. B1-a) Background removal processing can be performed, and (B1-c) contrast adjustment can be performed.

  In the present invention, the image 1 obtained by the step (B1) can be subjected to the following steps (B2) to (B4) as necessary. These are performed from the viewpoint of improving the accuracy or speed of the subsequent analysis, and are all optional steps. The order of these steps is not particularly limited, but preferably, the steps (B2), (B3), and (B4) can be performed in this order.

(B2) Masking process The masking process is not an essential process, but can be performed to reduce the background. Or when two or more colonies are contained in an analysis image, it can carry out in order to divide and analyze each colony.

  The masking process for reducing the background can be performed as follows. The image 1 is further binarized by contrast adjustment to separate the feeder region and the pluripotent stem cell region. In this case, for example, the feeder region can be black (or white) and the pluripotent stem cell colony region can be white (or black). Thereafter, image processing for filling voids that may occur in the pluripotent stem cell colony with white (or black) can be performed. Using the obtained image, image 1 may be masked to obtain an analysis image (image 3). However, when a plurality of pluripotent stem cell colonies exist in close proximity, a mask for each colony is further provided. The masking process can be performed after creating.

  In order to analyze each colony separately, the masking process can be performed as follows. For example, if watershed subdivision (Watershed) is performed, two or more connected colonies can be separated. Specifically, it calculates the Euclidean distance map (EDM) of the image, finds the final erosion point (UEP), enlarges its edge as much as possible, until the edge of the particle arrives, or other UEP's It can be expanded until it reaches the edge of the region to separate two or more connected colonies. After separating two or more adjacent colonies, a mask image (image 2) for each colony can be obtained for each colony. Using the mask (image 2) created for each colony, image 1 can be masked for each colony, and only the pluripotent stem cell colony to be evaluated can be extracted and used as an analysis image (image 3).

(B3) The image processing step (B3) of the embryoid body part is not necessarily performed after the masking process of step (B2), but from the viewpoint of accurately extracting the embryoid body part, It is preferable to carry out later. The pluripotent stem cell may form a colony with a portion that has not been fully expanded for about 2 days after seeding. The part that is not completely expanded is referred to herein as an embryoid body part, but the embryoid body part may adversely affect the analysis (for example, a good colony is determined to be a bad colony). Therefore, it can be removed by image processing. Thereby, in this invention, the analysis precision of the colony which has an embryoid body part improves. The image processing of the embryoid body part according to the present invention may be performed only on the colony including the embryoid body part, but it is not necessary to be limited to the colony including the embryoid body part. You may perform collectively with respect to the colony which does not contain a body-shaped part.

  Image processing of the embryoid body part can be performed as follows. First, void portions seen in the image 1 or 3 can be extracted by binarizing the image (image 4; FIG. 4E). Since the embryoid body-like part is accompanied by a sharp and clear contrast decrease, the binarization threshold can be easily set by those skilled in the art. Thereafter, by synthesizing the extracted image 4 with the image 3, an image (image 5) from which voids derived from the embryoid body portion are removed can be obtained. The image 4 can preferably be combined with the image 3 after being matched with the average value of the gradation around the embryoid body-like part in the image 3 to be an analysis image (image 5).

(B4) Resolution Reduction Processing According to the present invention, when it is desired to increase the analysis speed by automatic processing using a computer or the like, the resolution of the obtained image (image 1, 3 or 5, preferably image 3 or 5) is set. It can be reduced (the obtained image is referred to as image 6). For this purpose, for example, the pixels of the analysis image can be n × m pixels. n and m are preferably smaller in terms of analysis speed, but larger in number from the viewpoint of analysis accuracy, and can be appropriately set according to the desired analysis speed and analysis accuracy. . For example, n and m may be the same or different and can be 10 to 200, preferably 20 to 100, and more preferably 30 to 50. The resolution can be lowered using a method well known to those skilled in the art, but a method can be used in which the gray levels of surrounding pixels are averaged to integrate the pixels.

(C) Image analysis According to the present invention, the quality of the pluripotent stem cell colony can be evaluated based on the differential image obtained in the step (B). Specifically, according to the present invention, the evaluation of the quality of colonies of pluripotent stem cells is as follows:
(C1) Evaluating the quality of colonies of pluripotent stem cells based on the image pattern of the obtained differential image (image 1, 3, 5 or 6), or (C2) the obtained differential image (image 1, 3, 5 or 6), digitizing each pixel according to the gradation of each pixel, calculating the numerical value or numerical distribution of each pixel,
(C2-1) Evaluating the quality of the colony based on the numerical value of the central part of the colony and, in some cases, the numerical value of the peripheral part,
(C2-2) Evaluating the quality of the colony based on the numerical distribution, or (C2-3) The at least one type of fit function created in advance for any colony is compared with the numerical distribution of the colonies to be evaluated. Curve fitting and evaluating the quality of the colony. Step (C) of the present invention can be executed by a computer using statistical analysis software or the like. Hereinafter, the process (C1) and the process (C2) will be described separately.

(C1) After the image processing of the pluripotent stem cell colony based on the image pattern of the differential image, the obtained differential image (image 1, 3, 5 or 6, preferably image 3, 5 or 6 Preferably, the quality of the pluripotent stem cell colony can be evaluated based on the image pattern by comparing the image 6). Specifically, for example, based on the pattern of the obtained image, a colony that is uniform throughout or shows a dark image pattern at the center is evaluated as a good colony, and the center is in a ring shape. By evaluating a colony showing a thin pattern as a poor colony, the quality of a pluripotent stem cell colony can be evaluated. The evaluation of the quality of the pluripotent stem cell colony can be performed visually, but from the viewpoint of automation, it is preferably performed using a computer. When evaluating the quality of a pluripotent stem cell colony using a computer or the like, it can be easily determined using a known pattern recognition algorithm.

(C2) The pluripotent stem cell colony quality evaluation step (C2) by digitizing the differential image , first, the pixel image is digitized from the differential image obtained in step (B) according to the gradation of each pixel. The numerical value or numerical distribution of each pixel is calculated. Specifically, the obtained differential image (image 1, 3, 5 or 6, preferably image 3, 5 or 6, and more preferably image 6) is obtained by extracting some pixels of the colony and obtaining numerical values. Or all the pixels of the entire colony may be digitized. The method for extracting a part of the colony pixels is not particularly limited, and examples thereof include a method for extracting the central pixel part of the colony and a method for extracting the central and peripheral part pixels of the colony. . Digitization can be performed based on the gradation of each pixel, and can be performed with 2 ⁿ gradations in the case of an n-bit grayscale image. For example, in the case of an 8-bit grayscale image, digitization can be performed with 256 gradations. When it is desired to increase the analysis speed by automatic processing using a computer or the like, the number of data can be reduced by performing averaging processing similar to the image resolution reduction processing in steps (B) and (4) in this step as well. Can be made.

  The numerical value and numerical distribution of each pixel thus obtained are applied to the step (C2-1), the step (C2-2) or the step (C2-3), and the quality of the colony is evaluated. Hereinafter, the steps (C2-1), (C2-2), and (C2-3) will be described in detail.

(C2-1) In the pluripotent stem cell colony quality evaluation step (C2-1) based on the value of each pixel, the quality of the pluripotent stem cell colony is determined based on the value of each pixel obtained from the differential image. Can be evaluated. Specifically, the quality of the colony can be evaluated based on the numerical value of the central part of the colony and, in some cases, the numerical value of the peripheral part.

  Evaluation of the quality of a colony based on the numerical value of a colony center part can be performed as follows. That is, the quality of a colony can be evaluated by measuring the numerical value in 1 area | region of the center part of a colony, and comparing the magnitude between colonies. Specifically, a colony having a high numerical value in the central part can be evaluated as a good colony, and a colony having a low numerical value in the central part can be evaluated as a bad colony. In the evaluation, a threshold value is set, and a colony having a numerical value in the center exceeding the threshold value is determined as a good colony, and a colony having a value equal to or less than the threshold value can be determined as a bad colony. According to the present invention, when the threshold is set high, the contamination rate of defective colonies decreases, but the recovery rate of good colonies tends to decrease. Moreover, when the threshold is set low, the recovery rate of good colonies increases, but there is a tendency that the mixing rate of defective colonies also increases. Therefore, those skilled in the art can appropriately set the threshold according to the recovery rate of good colonies and the contamination rate of bad colonies.

  Moreover, the evaluation of the quality of a colony based on the numerical value of a colony center part and the numerical value of its peripheral part can be performed as follows. That is, the quality of the colony can be evaluated from the numerical values of at least one region in the central part of the colony and at least one region in the peripheral part. Specifically, a colony having a low numerical value in the central part and a high numerical value in the peripheral part can be evaluated as a bad colony, and a colony or a peripheral in which the numerical value in the central part is higher than the numerical value in the peripheral part. A colony equivalent to the numerical value of the part can be evaluated as a good colony. Thus, according to the present invention, the quality of the pluripotent stem cell colony can be evaluated based on the numerical value obtained at the beginning of the step (C2). In the evaluation, a threshold value is set, and a colony having a numerical value in the center exceeding the threshold value is determined as a good colony, and a colony having a value equal to or less than the threshold value can be determined as a bad colony.

  In the present specification, the “center portion” of a colony is, for example, when the colony is regarded as a circle, the radius is 3/4, preferably 2/3, more preferably 1/2, even more preferably, the radius of the colony. Can be a region inside a concentric circle with a radius of 1/3, most preferably 1/4. Further, the “peripheral part” means a peripheral part of the central part of the colony and is inside the colony. For example, the “peripheral part” is the outside of the central part of the colony when the colony is regarded as a circle, and the radius is 1/4, 1/3, 1/2, 2/3, or 3 A region outside the concentric circles with a radius of / 4 and inside the colony. The “peripheral part” may be a ring-shaped region, for example, a radius of 1/4 to 3/4, 1/3 to 2/3, or 1/2 to 2/3 of the radius of the colony. A ring-shaped region sandwiched between concentric circles. The equation of the circle can be obtained by curve fitting with respect to the colony outline by the least square method. According to the present invention, the “central part” (or “one region of the central part”) of the colony is preferably one point in the central part of the colony. One point in the central part of the colony may be one point obtained based on a certain rule, and is not particularly limited. For example, the center of the colony can be obtained as the center of the circle. In addition, the center of a colony can also be calculated | required as UEP in the watershed subdivision of a process (B) (2), for example.

(C2-2) The pluripotent stem cell colony quality evaluation step (C2-2) based on the numerical distribution pattern evaluates the pluripotent stem cell colony quality based on the numerical distribution obtained from the differential image. be able to. Evaluation of the quality of the pluripotent stem cell colony based on the numerical distribution obtained from the differential image can be performed as follows. That is, the quality of the colony can be evaluated by calculating the numerical distribution of the cells along a straight line passing through the central part of the colony and comparing the numerical distribution between the colonies. The comparison of the numerical distributions can be performed by graphing the numerical distributions, for example. The graphing of the numerical distribution is not particularly limited, but for example, by expressing the distribution as a bar graph or a point graph, for example, with the numerical value in the plane orthogonal coordinate system as the vertical axis and the straight line passing through the colony central part as the horizontal axis It can be carried out. The numerical distribution obtained in this way shows a convex shape in a good pluripotent stem cell colony, and shows a concave shape in the center of the colony in a bad colony, so based on the obtained numerical distribution pattern The quality of pluripotent stem cell colonies can be evaluated. The evaluation of the quality of the pluripotent stem cell colony can be performed visually, but from the viewpoint of automation, it is preferably performed using a computer. When evaluating the quality of a pluripotent stem cell colony using a computer or the like, it can also be easily determined using a known pattern recognition algorithm.

(C2-3) A pluripotent stem cell colony quality evaluation step (C2-3) based on an approximate expression for a numerical distribution is created in advance for a numerical distribution obtained along a straight line passing through the center of an arbitrary colony. The at least one kind of fit function can be curve-fitted to the numerical distribution of the colonies to be evaluated, and evaluated by evaluating the quality of the pluripotent stem cell colonies. Specifically, a fit function is created in advance for a numerical distribution of colonies that are judged good and / or bad by skilled engineers, and at least one type of fit function obtained is used. By performing curve fitting on the numerical distribution of the colonies to be evaluated, the quality of the colonies can be evaluated. For example, a pre-created fit function includes parameters for curve fitting and can be created to represent the cell density distribution of colonies judged good and / or bad by skilled technicians. it can. Such a fit function or approximate curve can be appropriately created by those skilled in the art with reference to the shape of the cell density distribution. The number of parameters in the fit function is not particularly limited, but can be about 2 to 10, for example. The curve fit can be performed using, for example, a least square method.

As a fitting function for a numerical distribution obtained from a colony determined to be good by a skilled engineer, for example, the position of a straight line passing through the center of the colony is the horizontal axis (X axis) of the plane orthogonal coordinate system, and the numerical value is the vertical axis When a graph of a fit function (y = f (x)) is created as (Y-axis), a fit function (f _good function) representing a convex shape is mentioned. In the present specification, “convex shape” means a convex shape in which a curved graph is represented by a good colony numerical distribution (for example, FIG. 5A). An example of a function of a convex shape, but are not limited to, for example, monotonously increased when x is less than x _a, takes a maximum value at a certain real number x _a, include monotonically decreasing function when x is greater than x _a It is done. Maximum value means that the value of f _{(x a)} that satisfies _{f (x a) ≧ f (} x) at x in the vicinity of _{x a (x a} is any real number). Therefore, in one aspect of the present invention, the f _good function is not only a function having a maximum value at one point of x = x _a , but the f _good function shows a constant value in a range where x is constant, and the constant value is A function having a maximum value, for example, a trapezoidal function having a maximum value in the entire portion corresponding to the upper base may be used. More specifically, as the f _good function, for example, in a colony having a diameter of 1 mm, a constant value is shown in a range of x = 300 μm to 700 μm, the constant value is a maximum value, and x <300 μm and x A function that does not take a maximum value in the range of> 700 μm can be mentioned. When curve fitting is performed on the colony to be evaluated, the f _good function preferably shows a good fitting for a good colony but does not show a good fitting for a bad colony.

The fitting function for the numerical distribution of colonies determined to be defective by a skilled engineer may be a fitting function (f _bad function) that shows a concave shape at the center of the colony and a convex shape at the periphery. it can. That is, the graph of the f _bad function indicates a shape in which one concave shape is sandwiched between two convex shapes. In this specification, the “concave shape” means a concave shape represented by a numerical distribution (for example, FIG. 5B) in the central part of the colony. An example of a concave function is not particularly limited, for example, a function x monotonously decreases when less than x _b, takes a minimum value at some real x _b, x increases monotonically when greater than x _b, namely And a function that takes only one minimum value in the center of the colony or in the whole area of x ( _xb is an arbitrary real number). Minimum value means that the value of f _{(x b)} satisfying _{f (x b) ≦ f (} x) at any x in the vicinity of _{x b.} Therefore, in the f _bad function, x may be a constant value within a certain range, and the constant value may take one maximum value or minimum value. Therefore, the “function having a concave shape in the central part of the colony and a convex shape in the peripheral part”, for example, increases monotonically as x increases and takes the first maximum value at a certain x _c. , and then monotonically decreases, takes one local minimum at a certain x _d, then further increases monotonically, taking a second maximum at a certain x _e, include then monotonically decreases function. In one embodiment of the present invention, the f _bad function is created so that x represents a constant value in a certain range and the constant value represents a maximum value or a minimum value. When the curve is fitted to the colony to be evaluated, the f _bad function preferably shows a good fitting for a bad colony but does not show a good fitting for a good colony.

  Therefore, according to the present invention, the quality of colonies of pluripotent stem cells can be evaluated by using a fit function for the numerical distribution of colonies.

In general, the goodness of curve fitting can be evaluated using as an index the degree of deviation between at least one kind of approximate curve obtained by curve fitting and the numerical distribution of colonies to be evaluated. Therefore, the present invention provides a method for evaluating the quality of colonies using as an index the degree of deviation between at least one kind of approximate curve obtained by curve fitting and the numerical distribution of colonies to be evaluated. The degree of deviation between the approximate curve obtained by curve fitting and the numerical distribution of the colonies to be evaluated (goodness of fitting of the approximate curve) can be evaluated using methods well known to those skilled in the art and evaluated visually. However, it may be evaluated using a mathematical method. When using a mathematical method, although not particularly limited, for example, χ ² / NDF (degree of freedom = number of fitted data−approximate expression) as an index of the degree of deviation between the approximate curve and the numerical distribution of the colony to be evaluated The quality of pluripotent stem cells can be determined by comparing the magnitudes of the parameters. Alternatively, as an index of the degree of deviation between the approximate curve and the numerical distribution of the colony to be evaluated, the average of the sum of squares of the difference between the measured value and the approximate curve is used, and the colonies of pluripotent stem cells are compared by comparing the magnitudes You may evaluate the quality of. The average of the sum of squares of the difference between χ ² / NDF and the actually measured value and the approximate curve tends to be smaller as the deviation of the curve fit is smaller. Therefore, using the degree of deviation between at least one kind of approximate curve obtained by curve fitting and the numerical distribution of the colonies to be evaluated as an index, the average of the sum of squares of the difference between χ ² / NDF or the actually measured value and the approximate curve The quality of colonies of pluripotent stem cells can be evaluated using the size of. Here, for example, if a threshold is set for the average of the sum of squares of differences from χ ² / NDF, measured values or approximate curves, the smaller the threshold, the lower the proportion of bad colonies evaluated as good. The larger the ratio, the higher the proportion of bad colonies that are evaluated as good. Therefore, those skilled in the art can appropriately set a threshold according to the recovery rate of good colonies and the contamination rate of bad colonies, and determine the quality of pluripotent stem cell colonies based on whether or not the threshold is exceeded. (See also the evaluation method based on parameter D below).

Thus, according to the present invention, the fit function created in advance shows a fitting function (f _good function) indicating a convex shape and / or a concave shape at the central part of the colony, and convex at the peripheral part. It is at least one type of fitting function including a fitting function ( _fbad function) indicating a shape (however, the position of a straight line passing through the center of the colony is the horizontal axis of the plane orthogonal coordinate system, and the numerical value is the vertical axis) Function graphs) and methods for assessing the quality of pluripotent stem cell colonies. The fit function used for the evaluation may be one type, but is preferably two or more types, more preferably, one or more types of colonies judged to be good by a skilled technician by a skilled technician. One or more types of colonies determined to be defective can be a total of two or more types. Therefore, according to the present invention, the fit function created in advance is a fit function (f _good function) indicating a convex shape, and a fit indicating a concave shape at the center of the colony and a convex shape at the periphery. It is at least two types of fitting functions including a function (f _bad function) (however, the position of a straight line passing through the center of the colony is the horizontal axis (X axis) of the plane orthogonal coordinate system, and the numerical value is the vertical axis (Y axis) And a graph of the fit function is prepared), and a method for evaluating the quality of the pluripotent stem cell colony is provided.

According to the present invention, the numerical distribution need not be considered for cells outside the colony. Therefore, it is sufficient that the fit function shows a good approximation at least within the colony. The f _good function and the f _bad function may be a function that converges to a constant value, a function that diverges, or a function that oscillates in the region outside the colony. However, the behavior of the function outside the colony affects the analysis. In this case, it is preferable to perform analysis after removing the area outside the colony. In this case, for example, the area where the measured value of the numerical distribution is 10 or less, 5 or less, 3 or less, or 0 is excluded from the colony. This area can be determined and excluded. Also, considering that the approximation target is a numerical distribution obtained from an image of a colony, the f _good function or the f _bad function of the present invention is preferably always 0 or more in the colony and outside the colony. It can be created to represent a numerical distribution that takes 0 or a value close to 0. Any of the above methods can reduce the adverse effect of the analysis due to the area outside the colony.

Therefore, according to the present invention, the f _good function is preferably a function representing a convex shape, and the following condition:
(Condition G1) Converge in the limits of x → −∞ and x → ∞.
(Condition G2) 0 or more for any real number x in the colony, and (Condition G3) One, two or all conditions selected from having one local maximum in the colony More preferably, it can be created so as to satisfy all the conditions. In the present specification, the “convergence function” is a constant value, preferably a value that is sufficiently small so as not to adversely affect the analysis (for example, a value of 15 or less, 10 or less, 5 or less, 1 or less, or 0 ). As an f _good function that satisfies all of the above conditions G1 to G3 and represents a convex shape, for example, an f _good function of the following formula:
(Where A ₀ , A ₁ , b and c are parameters and x is a variable),
(Where A ₀ , A ₁ , w and x ₀ are parameters and x is a variable),
(In the formula, A ₀ , A ₁ , a ₁ , a ₂ , x ₀ and x ₁ are parameters, and x is a variable.)
At least one function selected from the group consisting of As an f _good function that satisfies all of the above conditions G1 to G3 and represents a convex shape, a function (for example, a trapezoidal function) that has a constant function value at the center of the colony and exhibits a maximum value. ) Can also be suitably used. These f _good functions can be preferably used particularly for determining the quality of iPS cell colonies.

According to the present invention, the f _bad function represents a concave shape at the center of the colony and a convex shape at the periphery thereof (that is, one concave area is sandwiched between two convex areas. Or a function in which x indicating one minimum value is sandwiched between x indicating two maximum values), and preferably the following conditions:
(Condition B1) Converge in the limits of x → −∞ and x → ∞,
(Condition B2) Within a colony, it becomes 0 or more for any real number x, and
(Condition B3) It can be created so as to satisfy any one, two or all conditions selected from having one minimum value and two maximum values in the colony, more preferably all conditions Can be created to meet. For example, an f _bad function that represents a concave shape at the center of the colony, a convex shape at the periphery thereof, and satisfies any one or more of the above conditions B1 to B3 is, for example, a function f of the following formula: _bad (x):
(Where A ₀ , A ₁ , w ₁ , w ₂ , x ₁ and x ₂ are parameters and x is a variable),
(Where A ₀ , A ₁ , w, w ₁ , w ₂ , x ₁ and x ₂ are parameters and x is a variable),
(Where A ₀ , A ₁ , A ₂ , a ₁ , a ₂ , b ₁ , b ₂ , x ₁ and x ₂ are parameters and x is a variable), or
(In the formula, A ₀ , A ₁ , A ₂ , A ₃ , A ₄ , x ₀ are parameters, and x is a variable.)
It is. These _fbad functions can be preferably used particularly for determining the quality of iPS cell colonies.

  Further, according to the present invention, in order to improve the analysis accuracy, the quality of the colony of pluripotent stem cells can be evaluated based on the pixels of the entire colony. First, for convenience of analysis, the numerical values of the respective pixels that have been converted into numerical values can be handled together as a numerical matrix, for example (for example, FIGS. 2G, 3G, and 4G). From the obtained numerical matrix, a primary array of numbers in each row or each column can be extracted, and a fit function can be curve-fitted to each primary array. Curve fitting may be performed by extracting a part of the primary sequence. For example, for each colony, a primary sequence along a straight line passing through the central part of the colony is extracted and only the primary sequence is extracted. Or may be performed for all primary sequences.

(C2-4) Parameter setting and pass / fail evaluation of pluripotent stem cell colonies based on the parameters In the present invention, after the step (C2-3), the step (C2-4) is further performed as necessary. The quality of colonies of pluripotent stem cells can be evaluated. That is, according to the present invention, the quality of a pluripotent stem cell colony is evaluated by curve fitting both the f _good function and the f _bad function to a numerical distribution obtained along a straight line passing through the center of the colony. However, in the evaluation, if necessary, one or more parameters may be set from these functions, and the set parameters may be evaluated as an index. For example, as a parameter serving as an index for evaluating the pluripotent stem cells, in the colony, the maximum value of f _good function, the maximum value of f _bad function, the minimum value of f _bad function, the maximum value of the measured values and the measured The minimum value can be mentioned. Pluripotent stem cells may be evaluated using any one of these parameters as an index, or may be evaluated as an index by combining two or more of these parameters. When setting or combining the parameters, for example, the parameters can be set and combined so that the difference in the shape of the approximate curve graph between the good colonies and the bad colonies can be extracted. In particular, the approximate curve of the numerical distribution of bad colonies shows a characteristic concave shape in the central part of the colonies. Therefore, in the evaluation, it is preferable to set parameters so that the characteristic concave shape can be compared with the numerical distribution of defective colonies. For example, the numerical value of the central part of the colony reflecting the characteristic concave shape is measured. A value or an approximate value based on the f _bad function can be set as a useful parameter of an evaluation index of colony quality. As a combination of parameters, for example, any one or more of the maximum value of the f _good function in the colony, the maximum value of the f _bad function and the maximum value of the actual measurement value, and the minimum value or the actual measurement value of the f _bad function in the colony A combination with one or more of the minimum values can be mentioned. Alternatively, other parameter combinations include a combination of two or more parameters selected from the group consisting of the maximum value of the f _good function, the maximum value of the f _bad function, and the minimum value of the f _bad function in the colony. it can. After combining the parameters, the sum, difference, product or ratio of two or more parameters can be taken to further emphasize the difference between good and bad colonies. A new parameter can be created from the sum, difference, product or ratio of two or more parameters, and can be used for evaluation in combination with other parameters. Specifically, a parameter serving as an index for evaluating the quality of a pluripotent stem cell colony can be set as follows, for example. When calculating the sum and difference of parameters, weighting can be performed, or it can be performed without weighting.

A more specific example of how to combine parameters is not particularly limited,
Parameter A: Difference between the value of the f _good function and the value of the f _bad function in the central part of the colony (preferably, the difference between the value of the f _good function and the value of the f _bad function at the location where the f _bad function takes a minimum value) ,
Parameter B: difference between the maximum value and the minimum value of the f _bad function in the colony,
Parameter C: difference between the maximum measured value and the minimum measured value at the center of the colony,
Parameter D: root mean square of the difference between the _fgood function in the colony and the actual measurement value,
Parameter E: Parameter A + Parameter B + Parameter C + 0.2 × Parameter D
Etc. can be used.

  The above parameters A to E are all set appropriately so as to be small for colonies of good pluripotent stem cells in an undifferentiated state and large for poor pluripotent stem cells that have started differentiation. The parameter E is a parameter obtained by weighting and adding to the parameters A to D, but such weighting can be appropriately performed by those skilled in the art. In the present invention, as long as the parameter is a parameter that causes a difference between a good colony and a bad colony, regardless of the parameters A to E, those skilled in the art can freely set and use the parameter. be able to.

When evaluating the quality of a pluripotent stem cell colony based on the pixels of the entire colony according to the present invention, for example, the numerical matrix obtained by the step (C2-3) is row by row and / or column by column. Can be decomposed into a primary array of numerical values, and an approximate curve can be curve-fitted to each primary array. For example, when a parameter (for example, parameters A to E) is extracted from each primary array after curve fitting, n + m parameters are obtained for each parameter for each colony in the case of an n-by-m numeric matrix. . The obtained n + m parameters may be used for evaluation as they are. In that case, for example, the maximum value of the parameter (that is, the maximum value of the parameter based on the image of the entire colony) is used as the parameter value for each colony. be able to. Alternatively, in order to improve the accuracy of the evaluation by reducing the influence on the analysis due to sudden outliers, the following average processing and / or smoothing processing is further performed, and then the maximum value of each parameter is set. You may get it. That is, averaging is performed so that the value of the component (x _k , y _j ) is the geometric mean or arithmetic mean of the parameter value at x = x _{k and} the parameter value at y = y _j, and n rows Create an m-column numeric matrix. Furthermore, in order to reduce the influence on the analysis due to sudden outliers, the obtained numerical matrix of n rows and m columns can be smoothed. Smoothing is not particularly limited, for example,
This can be done by filtering using In the present invention, averaging with an oblique component is particularly effective, and a smoothing filter used in the present invention can be appropriately set by those skilled in the art. After or without performing the averaging process and / or smoothing process, the maximum value of the components of the numerical matrix can be calculated for each parameter, and this can be used as the parameter value for each colony. These parameters may be used for calculation of new parameters by further combining with or without weighting. The parameter E may be calculated based on the parameters A to D obtained after the averaging process and / or the smoothing process.

  According to the present invention, the quality of colonies formed by pluripotent stem cells can be evaluated by evaluating at least one of the obtained parameters (for example, parameters A to E). Here, for example, when a threshold value is set for each of the parameters A to E, the proportion of bad colonies that are evaluated as good decreases as the threshold value is decreased, and the failure that is evaluated as good as the value is increased. The percentage of colonies increases. Therefore, those skilled in the art can appropriately set a threshold according to the recovery rate of good colonies and the contamination rate of bad colonies, and determine the quality of pluripotent stem cell colonies based on whether or not the threshold is exceeded. Can do. Therefore, according to the present invention, the quality of the pluripotent stem cell colony can be evaluated using the above parameters (for example, parameters A to E).

  According to the present invention, (B) image processing of the obtained image, and (C) evaluation of the quality of the pluripotent stem cell colony based on the obtained image are performed by a computer or the like. Can be automated. Accordingly, a program for causing a computer to execute the method of the present invention is provided. Specifically, according to the present invention, a step (B) of obtaining a differential image based on an image of a pluripotent stem cell colony, and a step of automatically determining the quality of the pluripotent stem cell colony by analyzing the image A program for causing a computer to execute (C) is provided. The present invention also provides a computer-readable recording medium that records the program of the present invention. According to the present invention, there is further provided a computer for recording the program of the present invention in its internal recording device or an automatic determination system for quality of pluripotent stem cell colonies comprising the computer of the present invention.

  The program of the present invention may be recorded on a recording medium such as a flexible disk or a CD-ROM, and read and executed by a computer. The recording medium is not limited to a removable medium such as a magnetic disk or an optical disk, but may be a fixed recording medium such as a hard disk device or a memory. The program of the present invention may be distributed via a communication line (including wireless communication) such as the Internet. Further, the program may be distributed in a state where the program is encrypted, modulated or compressed, and stored in a recording medium via a wired line such as the Internet or a wireless line.

Example 1: Image processing of colonies formed by iPS cells In this example, image analysis methods for evaluating the quality of iPS cells were examined.

(Acquisition of iPS cell colony image by phase contrast microscopy)
In this example, human iPS cells (established strain by Kawasanada Laboratory, Cell Evaluation Group, Advanced Medical Promotion Foundation) were used as cells. Culturing was performed under two conditions: on-feeder conditions using a feeder and feeder-less conditions. SNL cells (manufactured by DS Pharma Biomedical, product number: EC07032801) were used as feeder cells. Under on-feeder conditions, the medium is a medium for human ES cell culture (Dulbecco's modified Eagle medium / nutrient mixture F-12 Ham (manufactured by Sigma Aldrich, product number: D6421), 500 mL, knockout serum substitute (manufactured by Invitrogen, product number) : 10828-028) 125 mL, non-essential amino acid solution (manufactured by Sigma-Aldrich, product number: M7145) 5 mL, 200 mM L-glutamine (manufactured by Invitrogen, product number: 25030-081) 6.25 mL, 0.1M 2-mercapto PBS supplemented with ethanol (Invitrogen, product number: 21985) 500 μL, bFGF (manufactured by Wako Pure Chemical Industries, product number: 064-04541) final concentration of 5 ng / mL, and feeder-less conditions, ReproFF2 medium (Repr oCell, product number: RCHEMD006) was added with bFGF (manufactured by Wako Pure Chemical Industries, product number: 064-0541) final concentration of 5 ng / mL. Previously, iPS cells were observed with an inverted phase contrast microscope IX81 (Olympus) equipped with a 4 × objective lens and a 10 × eyepiece, and the image was set at a resolution of 1.6 μm / pixel. The sample was taken into a PC using a digital camera (manufactured by Olympus, product number: DP72) and used for image analysis.In this example, 30 best iPS cell colonies, iPS cell colonies considered good Images were acquired for a total of 180 cases of 50 cases and 100 cases of iPS cell colonies regarded as defective.

(Image analysis)
Image analysis was performed using image processing software ImageJ (http://rsbweb.nih.gov/ij/) provided free of charge by the National Institutes of Health (NIH). For image analysis, an image obtained by phase contrast microscopy was first converted to an 8-bit (256 gradation) grayscale image.

  Next, image processing using a Sobel filter was performed on the obtained image. Specifically, after performing differential filter processing using a 3 × 3 Sobel filter using ImageJ, contrast adjustment is performed, then averaging processing is performed every 20 pixels, and after contrast adjustment is performed, rolling is performed. A background image was extracted using the ball algorithm, contrast adjustment was performed, and finally a 40 × 40 pixel image was converted to obtain a differential filtered image.

  As a result, it was possible to produce a clear difference in the pattern of images between the iPS cell colonies that were considered good (good colonies) and the iPS cell colonies that were not good (bad colonies) (FIGS. 1A and B). ). Specifically, an image with uniform gradation is obtained from a good iPS cell colony (FIG. 1A), but a ring-shaped image with a light gradation at the center is obtained from a poor iPS cell colony. (FIG. 1B). Moreover, it was possible to evaluate whether all the colonies subjected to the image processing were good or bad based on the differential filter processing image. From these results, it was suggested that image processing using a differential filter is effective in evaluating the quality of colonies of pluripotent stem cells.

The present inventors tried to perform differential filter processing of defective iPS cell colonies using various other differential filters. As a result, it became clear that the filter process was effective when any differential filter was used (FIGS. 1C to 1L). In addition to the known differential filter as described above, for example, the following improved Laplacian filter created by appropriately improving a Laplacian filter:
The differential filter processing was effective even when the differential filter processing was performed using (FIG. 1M).

  From this, it became clear that the differential filter processing of the phase contrast micrograph of the iPS cell colony is effective for evaluating the quality of the pluripotent stem cell colony regardless of the type of the differential filter. For the differential filter processing, a wide variety of filters can be used as long as the image conversion is based on the differentiation of the image, and it is considered that a differential filter obtained by improvement and other freely created differential filters can also be widely used.

Example 2: Image preprocessing for image analysis In this example, a masking process for extracting an image for each colony was performed.

  First, in order to create a mask for masking, binarization of the image is performed based on the images (FIGS. 2B, 3B, and 4B) obtained by the image processing by the 3 × 3 Sobel filter of Example 1. The feeder area (black) and the colony area (white) were separated. Thereafter, voids (black) that may occur in the colony region were filled with white (FIGS. 2C, 3C, and 4C).

  Next, when colonies exist adjacently connected, watershed subdivision (Watershed) is performed to separate two or more colonies and create a mask for each colony. Two or more colonies were isolated. Specifically, it calculates the Euclidean distance map (EDM) of the image, finds the final erosion point (UEP), enlarges its edge as much as possible, until the edge of the particle arrives, or other UEP's Expanding to reach the edge of the region, two or more connected colonies were separated. The obtained image was used as a mask for eliminating the background and other colonies. Then, the feeder area | region and other colony area | region of the image of Example 1 were masked using the obtained mask (FIG. 2D, 3D, and 4D).

Example 3: Image processing of an embryoid body (EB) -like part immediately after cell seeding Immediately after seeding, there may be an EB-like part that moves to black by microscopic observation. Since such a colony in which an EB-like site exists may be regarded as differentiated in the analysis, it is necessary to exclude the EB-like part by image processing. In this example, image processing for removing an embryoid body (EB) -like portion was performed.

  Phase contrast microscopic images of iPS cell colonies were obtained by the method described in Examples 1 and 2, and all phase contrast microscopic images were image processed using a differential filter (FIGS. 2B, 3B, and 4B). Next, by binarizing the obtained image, only the EB-shaped part was extracted (FIG. 4E). At this time, nothing was extracted from the EB-like site extraction process in the colonies having no EB-like site (FIGS. 2E and 3E).

  The masking image obtained in Example 2 (FIGS. 2D, 3D and 4D) and the EB-like part (FIGS. 2E, 3E and 4E) obtained by the extraction process of the EB-like part of Example 3 were synthesized ( Figures 2F, 3F and 4F). The treatment of Example 3 was performed on all iPS cell colonies to be analyzed.

Example 4 Image Analysis In this example, the differential image obtained in the example was analyzed.

  A square frame of 2 mm × 2 mm each in which the entire colony of the obtained masking image fits in the frame was set. Next, for the purpose of speeding up the calculation, the number of pixels was reduced by averaging the pixels to make the number of pixels in the square 40 pixels × 40 pixels. One pixel corresponds to a square of 50 μm × 50 μm. The obtained gray scale image (40 pixels × 40 pixels) was digitized from 0 to 255 according to the gradation and recorded as a 40 × 40 matrix (FIGS. 2G, 3G and 4G). Thereafter, 40 matrices of 1 × 40 columns corresponding to the 1st to 40th rows were created from the obtained matrix. Similarly, 40 matrices of 40 rows and 1 column corresponding to the 1st to 40th columns were created from the obtained matrix.

  The obtained 1 × 40 matrix and 40 × 1 matrix were graphed with the vertical axis as the size of the matrix component. Graphs of characteristic numerical distributions seen in good iPS cell colonies and bad iPS cell colonies are shown in FIGS. 5A and 5B, respectively.

In addition, in order to analyze the obtained matrix, an approximate expression was created for the characteristic numerical distributions indicated by good iPS cell colonies and bad iPS cell colonies, and curve fitting was performed for each of the 80 matrices obtained. did. The approximate expression is the following f _good (x) as a result of intensive studies.
(Where A ₀ , A ₁ , a ₁ , a ₂ , x ₀ and x ₁ are parameters and x is a variable), and f _bad (x):
(In the formula, A ₀ , A ₁ , A ₂ , A ₃ , A ₄ , x ₀ are parameters, and x is a variable.)
Was used.

In addition, the following four parameters were extracted from the curve fitting approximate expression (FIGS. 6A to 6D).
Parameter A: Difference between the value of f _good (x) and the minimum value of f _bad (x) at the center of the colony Parameter B: Difference between the maximum value and the minimum value of f _bad (x) within the colony Parameter C: Difference parameter D between the maximum value and the minimum value of the actually measured value at the center of the colony: root mean square of the difference between the value of f _good (x) in the colony and the actually measured value

Specifically, the parameter A is the value of the f _good function (here, the f _bad function) at the center of the colony after curve fitting of a numerical distribution is performed using the f _good function and the range of the iPS cell colony is defined. And the minimum value of the f _bad function were obtained, and the difference between them was used as parameter A. The parameter B is the difference between the maximum value and the minimum value of the f _bad function within the range defined as the colony range. The parameter C is a difference between the maximum value of the actually measured value within the range defined as the colony range and the minimum value of the actually measured value at the center of the colony, and the colony center is the center of the defined range. The parameter D was a curve distribution with a numerical distribution using the f _good function, and was the mean square of the difference between each measured value and the approximate expression within the range defined as the colony range.

In this way, after extracting the parameters A to D one by one for each row and each column, a 40 × 40 matrix was created for each of the obtained parameters A to D. The value of the (x _k , y _j ) component of the 40 × 40 matrix is the root mean square of the parameter value at x = x _{k and} the parameter value at y = y _j . The 40 × 40 matrix obtained for each parameter was filtered using the following matrix to smooth the numerical values.

  All parameters outside the colony range were set to zero.

  The maximum value of the matrix thus obtained was extracted for each parameter and used as the value of each parameter for further analysis.

  Furthermore, parameter E was defined as parameter A + parameter B + parameter C + 0.2 × parameter D, and parameter E was obtained for each colony. In this example, ROOT (CERN, http://root.cern.ch/drupal/) was used as numerical calculation software.

  As a result, as shown in FIG. 7, it was confirmed that the parameters A to E were all good iPS cell colonies and the values were low, and the bad iPS cell colonies were higher. Table 1 shows the values of parameters A to E for each example of good iPS cell colonies and bad iPS cell colonies.

  As shown in Table 1, the values of parameters A to E were large for the defective iPS cell colonies in the good iPS cell colonies and the bad iPS cell colonies.

  Furthermore, the result of examining the accuracy of determination when a threshold value is provided for each parameter and cells below the threshold value are determined to be good is as shown in FIG. In FIG. 8, the horizontal axis represents the threshold value of each parameter, and the vertical axis represents the recovery rate (%) of good iPS cell colonies determined to be good and the contamination rate (%) of bad iPS cell colonies. That is, when a threshold value is set for each of parameters A to E, cells below the threshold value are determined to be good, and cells exceeding the threshold value are determined to be defective, a good cell recovery rate and a bad cell contamination rate It is the figure which showed what the relationship becomes. The recovery rate of good cells and the contamination rate of bad cells were the ratio of cells judged good to the whole good cells and the percentage of cells judged good to the whole bad cells, respectively. . Table 2 summarizes the results of FIG.

  As shown in FIG. 8 and Table 2, it can be understood that as the recovery rate of good iPS cell colonies is increased, poor iPS cell colonies are mixed. Although any of the parameters A to D was used, the quality of the iPS cell colony could be evaluated. However, when the parameter E having the highest determination accuracy among the parameters was used for evaluation, a good iPS cell colony was recovered. If the rate is 90%, 6% of bad iPS cell colonies are mixed, if the recovery rate is 80%, 3% of bad iPS cell colonies are mixed, and if the recovery rate is 70%, poor iPS cell colonies It was found that when 3% of the cell colonies were mixed and the recovery rate was 60%, bad iPS cell colonies were not mixed. In particular, even when evaluation is performed without performing approximation using an approximate expression (parameter C), high-accuracy evaluation is possible. For example, if the recovery rate of good iPS cell colonies is 90%, the evaluation is poor. If 9% of iPS cell colonies are mixed and the recovery rate is 80%, 4% of bad iPS cell colonies are mixed. If the recovery rate is 70%, 3% of bad iPS cell colonies are mixed. It was found that when the recovery rate was 60%, 1% bad iPS cell colonies were mixed, and when the recovery rate was 30%, no bad iPS cell colonies were mixed.

  In this way, by applying differential filter processing to the phase difference image of the iPS cell colony, the iPS cell colony is used with or without the approximate expression (parameters A, B, D and E) (parameter C). Can be judged. Further, by combining the parameters (parameter E), it was possible to determine the quality of the iPS cell colony with higher accuracy.

Claims (25)

  A method for evaluating the quality of a pluripotent stem cell colony based on a differential filtering image (differential image) of a colony image formed by a pluripotent stem cell.   The method of Claim 1 which evaluates the quality of a colony based on the image pattern obtained from the differential image of the pluripotent stem cell.   From the differential image, digitization is performed for each pixel according to the gradation of each pixel, and then the quality of the colony is evaluated based on the numerical value of the central part of the colony and, in some cases, the numerical value of the peripheral part. The method described.   The method according to claim 1, wherein the differential image is digitized for each pixel according to the gradation of each pixel, and then the quality of the colony is evaluated based on the obtained numerical distribution.   From the differential image, digitization is performed for each pixel according to the gradation of each pixel, and then at least one type of fit function created in advance for the numerical distribution of colonies is curve-fitted to the numerical distribution of colonies to be evaluated The method of Claim 4 which evaluates the quality of the colony by doing. The fitting function created in advance is
A fitting function (f _good function) representing a convex shape, and / or
A fit function (f _bad function) that represents a concave shape at the center of the colony and a convex shape at the periphery.
(However, the position of the straight line passing through the colony center is the horizontal axis (X axis) of the plane orthogonal coordinate system, and the numerical distribution (Y axis) is the vertical axis. 6. The method of claim 5, wherein a graph is created. The method according to claim 6, wherein the fitting function created in advance is at least two types of fitting functions including an f _good function and an f _bad function. f _bad function is
(Condition B1) Converge in the limits of x → −∞ and x → ∞,
(Condition B2) Within a colony, it becomes 0 or more for any real number x, and
(Condition B3) The method according to claim 6 or 7, wherein any one, two or all of the conditions selected from having one minimum value and two maximum values in the colony are satisfied. f _bad function is
,
,
,and,
9. A method according to any one of claims 6 to 8 selected from the group consisting of: The f _bad function is
10. The method of claim 9, wherein f _good function is
(Condition G1) Converge in the limits of x → −∞ and x → ∞.
(Condition G2) 0 or more for any real number x in the colony, and (Condition G3) One, two or all conditions selected from having one local maximum in the colony The method according to any one of claims 6 to 10. f _good function is
,
,and,
12. A method according to any one of claims 6 to 11 selected from the group consisting of: f _good function is
The method of claim 12, wherein   The quality of a colony is evaluated using the degree of deviation between at least one kind of approximate curve obtained by curve fitting and the numerical distribution of a colony to be evaluated as an index. Method.   The method as described in any one of Claims 6-14 which evaluates the quality of a colony by using as a parameter | index the parameter extracted from the at least 1 type of approximate curve obtained by curve fitting. One or more parameters selected from the group consisting of the maximum value of the f _good function, the maximum value of the f _bad function, the minimum value of the f _bad function, the maximum value of the actual measurement value, and the minimum value of the actual measurement value in the colony The method of claim 15, wherein   The method according to claim 15 or 16, comprising evaluating the quality of the colony using the sum, difference, product or ratio of the two parameters as an index.   The value of the sum, difference, product, or ratio of two parameters and the sum, difference, product, or ratio of two parameters in another two parameter combination as an index. The method according to claim 17, comprising evaluating quality. The method according to claim 17 or 18, wherein the parameters are two parameters selected from the group consisting of a maximum value of the f _good function, a maximum value of the f _bad function, and a minimum value of the f _bad function in the colony. The following four parameters calculated for each colony from the approximate curve:
Parameter A: difference between the central value of the f _good function and the minimum value of the f _bad function,
Parameter B: difference between the maximum value and the minimum value of the f _bad function,
Parameter C: at least one selected from the group consisting of the maximum value of the actual measurement value and the minimum value of the actual measurement value at the center of the colony, and parameter D: the root mean square of the difference between the f _good function in the colony and the actual measurement value The method of Claim 18 which evaluates the quality of a colony based on a parameter.   21. The method according to claim 20, wherein the evaluation is based on a numerical value obtained by weighting and adding two or more parameters selected from the parameters A to D.   The program for making a computer perform the method as described in any one of Claims 1-21.   A computer-readable recording medium on which the program according to claim 22 is recorded.   A computer having the program according to claim 22 recorded in an internal storage device.   An automatic determination system for the quality of a pluripotent stem cell colony, comprising the computer according to claim 24.