Method for efficient collection and storage of experimental data

• US 8,090,748 B2
• Filed: 08/08/2008
• Issued: 01/03/2012
• Est. Priority Date: 11/13/1998
• Status: Expired due to Term

• Current Assignee: Cellomics Incorporated (Thermo Fisher Scientific Incorporated)
• Original Assignee: Cellomics Incorporated (Thermo Fisher Scientific Incorporated)
• Inventors: Boyce, Keith S., McKenna, Brian K., Glick, Phillip W., Dunlay, R. Terry
• Primary Examiner(s): Vy, Hung T
• Assistant Examiner(s): Cao, Phuong Thao
• Application Number:
  US12/188,967
• Publication Number:
  US 20080306989A1
• Time in Patent Office: 1,243 Days
• Field of Search: 707/102, 707/999.102, 707/803, 707/705, 707/795
• US Class Current: 707/803
• CPC Class Codes: G01N 15/1433 using image recognition
• CPC Class Codes: G01N 2015/1477 Multiparameters
• CPC Class Codes: G01N 2015/1497 Particle shape
• CPC Class Codes: G01N 2035/00158 Elements containing microarrays, i.e. "biochip"
• CPC Class Codes: G06V 20/69 Microscopic objects, e.g. biological cells or cellular parts

Abstract

Methods and system for efficient collection and storage of experimental data allow experimental data from high-throughput, feature-rich data collection systems, such as high-throughput cell data collection systems to be efficiently collected, stored, managed and displayed. The methods and system can be used, for example, for storing, managing, and displaying cell image data and cell feature data collected from microplates including multiple wells and a variety of bio-chips in which an experimental compound has been applied to a population of cells. The methods and system provide a flexible and scalable repository of experimental data including multiple databases at multiple locations including pass-through databases that can be easily managed and allows cell data to be analyzed, manipulated and archived. The methods and system may improve the identification, selection, validation and screening of new drug compounds that have been applied to populations of cells.

Claims

1. A method of storing experimental data on a computer system, comprising the steps of:

collecting a plurality of image data and a plurality of feature data from each of a plurality of sub-containers in a container, each sub-container having a biological specimen disposed therein or thereon;

creating a first database, wherein the first database includes links to other databases, and wherein the first database is used as a pass-through database by a display application to view data collected from the container;

creating a first entry in the first database linking the first database to a second database, wherein the second database includes;

configuration data used to collect data from the container,

summary data for the container calculated from the plurality of sub-containers, and

summary data for the sub-containers calculated from the plurality of image data and plurality of feature data, wherein the summary data for the sub-containers is organized in a plurality of tables, each table corresponding to a different one of the sub-containers; and

creating a plurality of second entries in the first database linking the first database to a plurality of third databases, wherein each third database includes a portion of the plurality of image data and the plurality of feature data collected from the plurality of sub-containers, and wherein the image and feature data for each third database is organized in a plurality of tables.

2. The method of claim 1, wherein the each biological specimens comprises a plurality of cells treated with an experimental compound.

3. The method of claim 1, wherein the container comprises a microplate, and the plurality of sub-containers comprise wells in the microplate.

4. The method of claim 1, wherein the container comprises a bio-chip and the plurality of sub-containers comprise selected micro-gels on the bio-chip.

5. The method of claim 1, wherein the biological specimen disposed within or on each sub-container comprises a plurality of cells, and wherein the plurality of feature data for each sub-container comprises a plurality of cell feature data for the plurality of cells in the corresponding sub-container and the plurality of image data for each sub-container comprises a plurality of photographic images collected from the plurality of cells in the corresponding sub-container.

6. The method of claim 1, wherein the first database does not include any data collected from the container.

7. The method of claim 1, wherein the first database comprises an application database comprising a plurality of pass-through tables corresponding to different containers and including a plurality of entries linking the application database to other databases.

8. The method of claim 1, wherein the second database comprises a system database comprising a plurality of database tables including any of:

plate, protocol, protocol assay parameter, protocol scan area, assay parameters, protocol channel, protocol channel reject parameters, manufacturer, form factor, plate feature, well, well feature, system or feature type database tables.

9. The method of claim 1, wherein each third database comprises a plurality of database tables including any of:

well, well feature, feature type well field, well field feature, well field feature image, cell or cell feature tables.

10. The method of claim 9, wherein each third database further includes any of plate, protocol, protocol assay parameter, protocol scan area, assay parameter, protocol channel, protocol channel reject parameter, manufacturer, form factor, plate feature, well system or feature type database tables.

11. The method of claim 1, wherein the step of collecting a plurality of image data and a plurality of feature data from each of the plurality of sub-containers comprises the steps of:

initializing the container using configuration information;

storing configuration information used for the container in the second database;

repeating steps (a)-(g) for each sub-container in the container;

(a) selecting an individual sub-container in the container,

(b) collecting a plurality of image data from the selected sub-container,

(c) storing the plurality of image data in the third database corresponding to the selected sub-container,

(d) collecting a plurality of feature data from the selected sub-container,

(e) storing the plurality of feature data in the third database corresponding to the selected sub-container,

(f) calculating a plurality of sub-container summary data using the plurality of image data and the plurality of feature data collected from the selected sub-container,

(g) storing the plurality of sub-container summary data in the second database,

calculating a plurality of container summary data for the container using the plurality of sub-container information from the second database; and

storing the plurality of container summary data in the second database.

12. The method of claim 1, wherein the first database is stored on a personal computer, the second database is stored on a database server and the plurality of third databases are stored on a shared database file server.

13. The method of claim 1, wherein the step of collecting a plurality of image data and a plurality of feature data from each of the plurality of sub-containers includes collecting a plurality of photographic image data and a plurality of cell feature data for a plurality of cells from a plurality of wells in a microplate for a pre-determined assay for an experimental compound.

14. The method of claim 1, wherein the portion of the plurality of image data and the plurality of feature data included in each third database comprises the plurality of image data and the plurality of feature data corresponding to a separate one of the sub-containers.

15. The method of claim 10, further comprising archiving and copying one or more of the third databases to another computer system for review without copying the second database to the other computer system.

16. A computer readable medium having stored therein instructions for causing a central processing unit to execute a method of:

collecting a plurality of image data and a plurality of feature data from each of a plurality of sub-containers in a container, each sub-container having a biological specimen disposed therein or thereon;

creating a first database, wherein the first database includes links to other databases, and wherein the first database is used as a pass-through database by a display application to view data collected from the container;

creating a first entry in the first database linking the first database to a second database, wherein the second database includes;

configuration data used to collect data from the container,

summary data for the container calculated from the plurality of sub-containers, and

summary data for the sub-containers calculated from the plurality of image data and plurality of feature data, wherein the summary data for the sub-containers is organized in a plurality of tables, each table corresponding to a different one of the sub-containers; and

creating a plurality of second entries in the first database linking the first database to a plurality of third databases, wherein each third database includes a portion of the plurality of image data and the plurality of feature data collected from the plurality of sub-containers, and wherein the image and feature data for each third database is organized in a plurality of tables.