Cell lineage extracting method

• US 7,110,584 B2
• Filed: 12/04/2000
• Issued: 09/19/2006
• Est. Priority Date: 03/23/2000
• Status: Expired due to Fees

• Current Assignee: Japan Science And Technology Corpration
• Original Assignee: Japan Science And Technology Corpration
• Inventors: Onami, Shuichi, Hamahashi, Shugo, Miyano, Satoru, Kitano, Hiroaki
• Primary Examiner(s): Wu, Jingge
• Assistant Examiner(s): Tabatabai, Abolfazl
• Application Number:
  US10/182,429
• Publication Number:
  US 20030108230A1
• Time in Patent Office: 2,115 Days
• Field of Search: 382128-134, 600/310, 600/407, 600/473, 600/476, 435/6, 435/7.1, 435/7.2, 435/7.21, 435/7.23, 435/40.5, 435/1.2, 435/40.51, 435/41, 435/70.1, 435/70.2, 435/70.3, 435/70.4, 435/440.449, 435451-455, 436/63, 436/74, 436/94, 436/519, 424/9.2
• US Class Current: 382/128
• CPC Class Codes: G01N 33/5005 involving human or animal cells immunoassay G01N33/56966; immunoassays of protozoa G01N33/56905; protozoa in screening assays C12Q1/025
• CPC Class Codes: G06T 2200/04 involving 3D image data
• CPC Class Codes: G06T 2207/10016 Video; Image sequence
• CPC Class Codes: G06T 2207/10056 Microscopic image
• CPC Class Codes: G06T 2207/30024 Cell structures in vitro; Tissue sections in vitro
• CPC Class Codes: G06T 7/11 Region-based segmentation
• CPC Class Codes: G06V 20/695 Preprocessing, e.g. image segmentation

Abstract

The present invention provides a method for constructing cell lineage that is less labor intensive and requires less time as a result of using a computer. The method comprises the step for obtaining a plurality of 2D images different in focal plane and a time by taking a plurality of the 2D images by changing the focal plane and taking a plurality of the 2D images in a time series for a cell constituting the subject of observation. The method further comprises the steps of extracting a nucleus area by carrying out image processing for individual 2D images; unifying the nucleus area, which is derived from the identical nucleus, from the nucleus area extracted from the individual 2D images; and constructing the cell lineage from a time and a position, where the nucleus area appears and disappears in the image, in the unified nucleus area.

Claims

1. A method for constructing a cell lineage comprising the steps of:

(a) obtaining a plurality of 2D images different in focal plane and time by taking a plurality of 2D images changing the focal plane and taking a plurality of 2D images in a time series for a cell constituting the subject of observation;

(b) extracting a nucleus area by carrying out image processing for individual 2D images;

(c) unifying the nucleus area extracted from the individual 2D images, which is derived from an identical nucleus; and

(d) constructing the cell lineage from a time and a position, where the nucleus area emerges and disappears in the image, in the unified nucleus area.

2. The method as claimed in claim 1, wherein the image is taken by a DIC microscope.

3. The method as claimed in claim 1, wherein the step for extracting comprises image processing that utilizes the difference in the brightness of the image between the nucleus and the remaining part of the cell.

4. The method as claimed in claim 3, wherein the step for extracting comprises detecting an area where the brightness variation in the image is poor as a nucleus.

5. The method as claimed in claim 4, wherein said detecting comprises one or more filters selected from the group consisting of a Kirsh filter, Prewitt filter, and FFT filter.

6. The method as claimed in claim 1, wherein the step for extracting comprises extracting a part where the intensity is large in a wide range along the incident angle of light as a nucleus.

7. The method as claimed in claim 6, the extracting comprises a step for taking a difference in a sum of intensity value of a predetermined top and bottom pixel along a seeming direction of light.

8. The method as claimed in claim 7, wherein the method comprises the steps of extracting a cell boundary and extracting an embryo area and wherein the result obtained by the method in claim 7 may be corrected based on the result obtained by the method in claim 7.

9. The method as claimed in claim 1, wherein the step for extracting comprises a plurality of different nucleus detecting algorithms and wherein an area recognized as a nucleus by any one of the algorithms is determined as the nucleus area in the image processing system as a whole.

10. The method as claimed in claim 1, wherein the extracting comprises the steps of:

partitioning the cell image by a small window;

scanning the image by calculating entropy of the window; and

extracting the nucleus area from the image.

11. The method as claimed in claim 1, wherein the unifying comprises the steps of:

unifying nucleus areas, which are derived from identical nucleus, contained in an image group on an identical focal plane;

unifying nucleus areas, which are derived from identical nuclei, contained in an image group at an identical time; and

further unifying the nucleus areas obtained by said two steps.

12. The method as claimed in claim 11, wherein the step for unifying the nucleus areas obtained by said two steps comprises unifying the nucleus areas in the case where there exists a combination of unified nucleus areas, which have a common nucleus area, between the nucleus areas unified in both the time series and the focal direction, these are regarded as a unified nucleus area derived from an identical nucleus, and are further unified.

13. The method as claimed in claim 1, wherein the constructing comprises detecting a parent cell and a daughter cell after division of the parent cell by obtaining a 4D distance between the nucleus areas.

14. A method for constructing a cell lineage comprising the steps of:

(a) obtaining a plurality of 2D images different in focal plane and a time by taking a plurality of the 2D images by changing the focal plane and taking a plurality of the 2D images in a time series for a cell constituting the subject of observation;

(b) extracting a nucleus area by carrying out image processing for individual 2D images;

(c) unifying the nucleus area, which is derived from the identical nucleus, from the nucleus area extracted from the individual 2D images;

(d) constructing the cell lineage from a time and a position, where the nucleus area emerges and disappears in the image, in the unified nucleus area; and

wherein

(e) said step (b) comprises the steps of;

extracting the area to become a candidate of the nucleus;

designating a presumable nucleus area by a trial operation of cell lineage preparation; and

extracting the nucleus area by feedback of the presumable area to the nucleus candidate area.

15. The method as claimed in claim 14, wherein the trial operation of cell lineage preparation includes at least one of unifying nucleus areas in an identical time and an identical focal plane, unifying 4D nucleus areas, and preparing the cell lineage, thereby allowing feedback of the designation of the presumable nucleus area by the trial operation.

16. The method as claimed in claim 15, wherein the feedback from unifying nucleus areas in an identical time and an identical focal plane comprises the steps of:

choosing the nucleus area;

unifying the nucleus areas in the identical time and the identical focal plane;

designating the nucleus candidate area; and

feeding the result of the designation of the presumable nucleus area to the step for choosing the nucleus area.

17. The method as claimed in claim 15, wherein the feedback from unifying 4D nucleus areas comprises the steps of:

choosing a 3D nucleus area;

unifying 4D.

18. The method as claimed in claim 15, wherein the feedback from preparing the cell lineage comprises the steps of:

choosing a 4D nucleus area;

preparing the cell lineage;

designating the nucleus candidate area; and

feeding the result of the designation of the presumable nucleus area to the step for choosing the nucleus area.

19. The method as claimed in claim 14, wherein said nucleus candidate area is given with a nucleus score and the nucleus area is extracted by comparing the nucleus score and a predetermined specified value, and wherein the nucleus score is to be changed by the feedback of the presumable nucleus area.

20. The method as claimed in claim 14, wherein the step for extracting the nucleus candidate area comprises the steps of:

image-processing the image using the difference in the brightness of the image regarding the nucleus and the remaining part of the cell;

designating the nucleus candidate area; and

giving the nucleus score to the nucleus candidate area.

21. The method as claimed in claim 20, wherein the extracting the nucleus candidate area comprises designating the nucleus area by binarizing the result obtained by the image processing using a predetermined threshold and the nucleus score is given to the designated area.

22. The method as claimed in claim 20, wherein the extracting the nucleus candidate area comprising extracting polar areas in a direction of black in the resultant image obtained after the image processing accompanying a score as the nucleus candidate area. nucleus areas;

designating the nucleus candidate area; and

feeding the result of the designation of the presumable nucleus area to the step for choosing the nucleus area.