Data structure of an image storage and retrieval system

• US 8,582,924 B2
• Filed: 06/30/2004
• Issued: 11/12/2013
• Est. Priority Date: 06/30/2004
• Status: Expired due to Fees

• Current Assignee: Carl Zeiss Microscopy GmbH (Carl-Zeiss-Stiftung)
• Original Assignee: CARL Zeiss Microimaging GmbH (Carl-Zeiss-Stiftung)
• Inventors: De La Torre-Bueno, Jose, Perz, Cynthia B.
• Primary Examiner(s): TSAI, TSUNG YIN
• Application Number:
  US10/882,661
• Publication Number:
  US 20060002636A1
• Time in Patent Office: 3,422 Days
• Field of Search: 382/305, 382133-134, 382128-129
• US Class Current: 382/305
• CPC Class Codes: G02B 21/367 providing an output produced by processing a plurality of individual source images, e.g. image tiling, montage, composite images, depth sectioning, image comparison

Abstract

Disclosed is an imaging system that stores and retrieves very large scanned digital images, as in applications that automatically scan biological samples using a computer-controlled digital camera microscope. Slide data is entered, zelle data is captured and compressed and a zelle database file is loaded. Furthermore, an image database file is loaded and it is determined whether another zelle is to be stored. The image can be retrieved by accessing the zelle database, reading a zelle record, reading an image file, loading the display buffer, and determining whether another zelle is to be loaded.

Claims

1. A method of storing a digital image acquired by a computer-controlled digitizing microscope, comprising:

partitioning a microscopic image into a matrix of zelles, wherein each zelle comprises a discrete portion of the microscopic image and each zelle includes a plurality of pixels of the microscopic image;

for each zelle, capturing attribute data descriptive of an associated zelle and capturing image data descriptive of a discrete portion of the microscopic image contained in the associated zelle;

for each zelle, determining whether said zelle contains specimen content therein;

classifying each zelle either partially or fully including specimen content therein as having information of interest and classifying each zelle not including any specimen content therein as not having information of interest;

compressing the image data;

storing the attribute data in a zelle database comprised of at least one zelle database file, each zelle database file being associated with at least one corresponding zelle; and

storing the compressed image data in an image database comprised of at least one image file, wherein each image file is associated with a corresponding zelle database file.

2. A method as defined in claim 1, wherein said compressing comprises a first process including restoring variations in color values for non-valuable colors to be uniform and a second process including a modified Classic Huffman Shift compression algorithm.

3. A method as defined in claim 2, wherein said non-valuable color comprises white.

4. A method as defined in claim 1, wherein the zelle database file contains one or more zelle records and wherein each zelle record further includes a plurality of record fields comprising binary digital data.

5. A method as defined in claim 4, wherein each zelle record field relates to one or more individual attributes of its at least one corresponding zelle.

6. A method as defined in claim 4, wherein each zelle record has a zelle pointer that identifies a single image file that possesses unique image data of the zelle associated with that zelle record.

7. A method as defined in claim 1, wherein the attribute data includes at least one of the group consisting of an identification number of a scanned microscope slide, coordinates for the associated zelle, a scale factor, area of the associated zelle, and an image file address where the image data for the associated zelle is stored.

8. A method as defined in claim 1, wherein the zelle database and the image database comprise non-volatile computer memory residing on a physical hard drive.

9. A method as defined in claim 1, wherein the zelle database and the image database comprise a single database.

10. A method as defined in claim 1, further comprising:

accessing at least one zelle database file for the microscopic image to obtain attribute data relating to a selected zelle;

accessing at least one image file associated with the zelle record to obtain image data associated with the selected zelle.

11. A method as defined in claim 1, wherein only zelles containing information of interest are compressed.

12. A non-transitory computer readable medium encoded with a computer program comprising instructions to cause a computer to:

partition a microscopic image into a matrix of zelles, wherein each zelle comprises a discrete portion of the microscopic image and wherein each zelle includes a plurality of pixels of the microscopic image;

for each zelle, capture attribute data descriptive of an associated zelle and capture image data descriptive of a discrete portion of the microscopic image contained in the associated zelle;

for each zelle, determine whether said zelle contains specimen content therein;

classifying each zelle either partially or fully including specimen content therein as having information of interest and classifying each zelle not including any specimen content therein as not having information of interest;

compress the image data for each zelle;

store the attribute data in a zelle database comprised of at least one zelle database file, each zelle database file being associated with at least one corresponding zelle; and

store the compressed image data in an image database comprised of at least one image file, wherein each image file is associated with a corresponding zelle database file.

13. A non-transitory computer readable medium as defined in claim 12, wherein the image data is compressed pursuant to two processes, including a first process including restoring variations in color values for non-valuable colors to be uniform and a second process including a modified Classic Huffman Shift compression algorithm.

14. A non-transitory computer readable medium as defined in claim 12, wherein the zelle database file contains one or more zelle records and wherein each zelle record further includes a plurality of, record fields comprising binary digital data.

15. A non-transitory computer readable medium as defined in claim 14, wherein each zelle record field relates to one or more individual attributes of its at least one corresponding zelle.

16. A non-transitory computer readable medium as defined in claim 14, wherein each zelle record has a zelle pointer that identifies a single image file that possesses unique image data of the zelle associated with that zelle record.

17. A non-transitory computer readable medium as defined in claim 12, wherein the attribute data includes at least one of the group consisting of an identification number of a scanned microscope slide, coordinates for the associated zelle, a scale factor, area of the associated zelle, and an image file address where the image data for the associated zelle is stored.

18. A non-transitory computer readable medium as defined in claim 12, wherein the instructions further cause the computer to:

access at least one zelle database file for the microscopic image to obtain attribute data relating to a selected zelle; and

access at least one image file associated with the zelle record to obtain image data associated with the selected zelle.

19. A microscope imaging system comprising:

a computer comprising;

a processor;

a computer program on computer readable medium, the computer program comprising instructions to cause the computer to;

partition a microscopic image into a grid of zelles, wherein each zelle comprises a discrete portion of the microscopic image and wherein each zelle includes a plurality of pixels of the microscopic image;

for each zelle, capture attribute data descriptive of an associated zelle and capture image data descriptive of a discrete portion of the microscopic image contained in the associated zelle;

for each zelle, determine whether said zelle contains specimen content therein;

classify each zelle either partially or fully including specimen content therein as having information of interest and classify each zelle not including any specimen content therein as not having information of interest;

compress the image data for each zelle;

store the attribute data in a zelle database comprised of at least one zelle database file, each zelle database file being associated with at least one corresponding zelle; and

store the compressed image data in an image database comprised of at least one image file, wherein each image file is associated with a corresponding zelle database file.

20. A system as defined in claim 19, wherein the image data is compressed pursuant to two processes, including a first process including restoring variations in color values for non-valuable colors to be uniform and a second process including a modified Classic Huffman Shift compression algorithm.

21. A system as defined in claim 19, wherein the zelle database file contains one or more zelle records and wherein each zelle record further includes a plurality of record fields comprising binary digital data.

22. A system as defined in claim 21, wherein each zelle record field relates to one or more individual attributes of its at least one corresponding zelle.

23. A system as defined in claim 21, wherein each zelle record has a zelle pointer that identifies a single image file that possesses unique image data of the zelle associated with that zelle record.

24. A system as defined in claim 19, wherein the attribute data includes at least one of the group consisting of an identification number of a scanned microscope slide, coordinates for the associated zelle, a scale factor, area of the associated zelle, and an image file address where the image data for the associated zelle is stored.

25. A system as defined in claim 19, wherein the instructions further cause the computer to:

access at least one zelle database file for the microscopic image to obtain attribute data relating to a selected zelle; and

access at least one image file associated with the zelle record to obtain image data associated with the selected zelle.