Automated Processing of chemical arrays and systems therefore

• US 20060064246A1
• Filed: 09/20/2004
• Published: 03/23/2006
• Est. Priority Date: 09/20/2004
• Status: Abandoned Application

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Ghosh, Jayati, Zhou, Xiangyang, Medberry, Scott Lee
• Application Number:
  US10/946,142
• Publication Number:
  US 20060064246A1
• Time in Patent Office: Days
• US Class Current: 702/19
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Abstract

Methods, systems and computer readable media for automatically generating information from chemical arrays. A plurality of image files representative pf features contained on a plurality of substrates, respectively, may be automatically and sequentially generated. Automatic and sequential feature extraction of the image files may be carried out, wherein automatic feature extracting of a first of the automatically generated image files is begun immediately after completion of the generation of that image file while a next substrate is being processed for automatic generation of a next image file therefrom. Methods, systems and computer readable media are provided for automatically generating information from chemical arrays, to include identifying an entity selected from the group consisting of data structures, directories, subdirectories and drives into which image files created from reading the chemical arrays are to be stored; polling the entity for the presence of a next new image file not identified in a most recent previous polling of the entity; automatically feature extracting the next new image file; outputting results from the step of automatically feature extracting the next new image file; iterating the step of polling the entity until a next new image is identified or until a predetermined time or predetermined number of polls have been reached; and repeating the steps of automatically feature extracting, outputting results and iterating polling when a next new image file is identified prior to passage. of the predetermined time or completion of the predetermined number of polls with an iteration.

Claims

1. A method of automatically generating information from chemical arrays, said method comprising the steps of:

automatically and sequentially generating a plurality of image files representative of features contained on a plurality of substrates or substrate regions, respectively;

automatically and sequentially feature extracting the image files, wherein automatic feature extracting of a first of the automatically generated image files is begun immediately after completion of the generation of that image file while a next substrate or substrate region is being processed for automatic generation of a next image file therefrom.

2. The method of claim 1, wherein said automatically and sequentially feature extracting the image files comprises automatically assigning a grid template and a protocol to each image file, each said image file being feature extracted according to the grid template and protocol assigned thereto.

3. The method of claim 2, comprising automatically assigning at least one of a grid file and a protocol to at least one image file in said plurality of image files that is different from at least one of a grid file and a protocol, respectively automatically assigned to at least one other image file in said plurality of image files.

4. The method of claim 2, wherein at least one of said automatic assignments of a grid template and protocol is made based on an identifier associated with the image to which the assignment is made, said identifier being linked with the assigned grid template and protocol.

5. The method of claim 1, wherein said automatically and sequentially feature extracting the image files comprises automatically and sequentially pre-processing and post-processing the image files, wherein automatic post-processing of a first of the automatically pre-processed image files is begun immediately after completion of the pre-processing of that image file while a next image file is being pre-processed.

6. The method of claim 1, wherein said image files are automatically and sequentially generated by scanning the substrates.

7. The method of claim 1, wherein the features contained on each substrate are contained in one or more arrays on each substrate.

8. The method of claim 7, wherein the arrays are polynucleotide or peptide arrays.

9. The method of claim 1, further comprising designating a selected subset of said plurality of image files generated to be outputted to a storage location where the selected subset of image files will not be automatically and sequentially feature extracted, wherein said step of automatically and sequentially feature extracting the image files is carried out on the remainder of the plurality of image files that do not belong to the selected subset.

10. A method comprising forwarding a result obtained from the method of claim 1 to a remote location.

13. A method comprising transmitting data representing a result obtained from the method of claim 1 to a remote location.

14. A method comprising receiving a result obtained from a method of claim 1 from a remote location.

15. A method of automatically generating information from chemical arrays, said method comprising the steps of:

identifying an entity selected from the group consisting of data structures, directories, subdirectories and drives into which image files created from reading the chemical arrays are to be stored;

polling the entity for the presence of a next new image file not identified in a most recent previous polling of the entity;

automatically feature extracting the next new image file;

outputting results from said step of automatically feature extracting the next new image file;

iterating said step of polling the entity until a next new image is identified or until a predetermined time or predetermined number of polls have been reached; and

repeating said steps of automatically feature extracting, outputting results and iterating polling when a next new image file is identified prior to passage of the predetermined time or completion of the predetermine number of polls with an iteration.

16. The method of claim 15, wherein the step of automatically feature extracting the next new image file comprises:

automatically pre-processing the next new image file;

outputting results of said pre-processing to an output entity selected from the group consisting of data structures, directories, subdirectories and drives, wherein said output entity may be the same as or different from said entity;

polling the output entity for the presence of a next new pre-processing results output not identified in a most recent previous polling of the entity; and

automatically post-processing the next new pre-processing results while automatic pre-processing of the next new image file is being carried out.

17. The method of claim 16, further comprising outputting post-processing results to a post-processing entity which is the same as or different from said entity and is the same as or different from said output entity;

polling the output entity for the presence of a next new pre-processing results output not identified in a most recent previous polling of the entity; and

automatically post-processing the next new pre-processing results.

18. The method of claim 15, wherein said automatic feature extraction includes automatically assigning a grid template and a protocol to each image file, each said image file being feature extracted according to the grid template and protocol assigned thereto.

19. The method of claim 18, comprising automatically assigning at least one of a grid file and a protocol to at least one of the image files that is different from at least one of a grid file and a protocol, respectively automatically assigned to at least one other of the image files.

20. The method of claim 18, wherein at least one of said automatic assignments of a grid template and protocol is made based on an identifier associated with the image to which the assignment is made, said identifier being linked with the assigned grid template and protocol.

21. The method of claim 15, wherein at least one of said image files contains multiple arrays.

22. A system for automatically generating information from chemical arrays, said system comprising:

an image production processor configured to automatically and sequentially generate a plurality of image files representative of features contained on a plurality of substrates or substrate regions, respectively; and

a feature extraction processor configured to automatically and sequentially feature extract the image files;

wherein automatic feature extracting of a first of the automatically generated image files is begun immediately after completion of the generation of that image file.

23. The system of claim 22, wherein said image production processor and said feature extraction processor are embodied by a single processor, and wherein image production of a next substrate or substrate region is automatically carried out after completion of feature extraction processing of a previous image, wherein said image production and feature extraction are carried out in the order stated, alternating automatically and sequentially.

24. The system of claim 22, wherein said image production processor processes a next substrate or substrate region for automatic generation of a next image file therefrom while said feature extraction processor processes the previous image.

25. The system of claim 22, comprising a plurality of image production processors, wherein said image production processors cooperate to automatically and sequentially generate the plurality of image files.

26. The system of claim 22, comprising a plurality of feature extraction processors, wherein said feature extraction processors cooperate to automatically and sequentially process the plurality of image files for feature extraction.

27. The system of claim 22, further comprising a storage entity into which the image files are stored upon production thereof, wherein said feature extraction processor automatically and sequentially accesses the image files in said storage entity to feature extract the image files.

28. The system of claim 22, comprising a plurality of image production processors, wherein said image production processors cooperate to automatically and sequentially generate the plurality of image files;

a storage entity into which the image files are stored upon production thereof by said image production processors; and

a plurality of feature extraction processors, wherein said feature extraction processors cooperate to automatically and sequentially process the plurality of image files for feature extraction, and wherein said feature extraction processors automatically and sequentially accesses the image files in said storage entity to feature extract the image files.

29. A computer readable medium carrying one or more sequences of instructions for automatically generating information from chemical arrays, wherein execution of one or more sequences of instructions by one or more processors causes the one or more processors to perform the steps of:

automatically and sequentially generating a plurality of image files representative of features contained on a plurality of substrates or substrate regions, respectively;

automatically and sequentially feature extracting the image files, wherein automatic feature extracting of a first of the automatically generated image files is begun immediately after completion of the generation of that image file while a next substrate or substrate region is being processed for automatic generation of a next image file therefrom.