System and Method for Data Management in a Linear-Array-Based Microscope Slide Scanner

• US 20070036462A1
• Filed: 04/21/2006
• Published: 02/15/2007
• Est. Priority Date: 05/03/2000
• Status: Active Grant

• Current Assignee: Leica Biosystems Imaging Inc. (Danaher Corporation)
• Original Assignee: Aperio Technologies Incorporated (Danaher Corporation)
• Inventors: Crandall, Greg, Olson, Allen, Eichhorn, Ole, Soenksen, Dirk
• Granted Patent: US 7,428,324 B2
• Time in Patent Office: Days
• US Class Current: 382/284
• CPC Class Codes: G02B 21/002 Scanning microscopes scanning near field optical microscopes G01Q60/18
• CPC Class Codes: G02B 21/0036 Scanning details, e.g. scanning stages
• CPC Class Codes: G02B 21/008 Details of detection or image processing, including general computer control
• CPC Class Codes: G02B 21/14 affording illumination for phase-contrast observation
• CPC Class Codes: G02B 21/245 using auxiliary sources, detectors
• CPC Class Codes: G02B 21/26 Stages; Adjusting means therefor
• CPC Class Codes: G02B 21/32 Micromanipulators structurally combined with microscopes
• CPC Class Codes: G02B 21/34 Microscope slides, e.g. mounting specimens on microscope slides
• CPC Class Codes: G02B 21/365 Control or image processing arrangements for digital or video microscopes G02B21/361, G02B21/362 take precedence
• 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
• CPC Class Codes: H04N 1/053 in main scanning direction, e.g. synchronisation of line start or picture elements in a line
• CPC Class Codes: H04N 1/1903 Arrangements for enabling electronic abutment of lines or areas independently scanned by different elements of an array or by different arrays
• CPC Class Codes: H04N 1/193 using electrically scanned linear arrays , e.g. linear CCD arrays
• CPC Class Codes: H04N 1/19573 Displacing the scanned image
• CPC Class Codes: H04N 2201/04727 on a linear encoder
• CPC Class Codes: H04N 2201/04755 by controlling the position or movement of a scanning element or carriage, e.g. of a polygonal mirror, of a drive motor
• CPC Class Codes: H04N 23/56 provided with illuminating means
• CPC Class Codes: H04N 23/631 Graphical user interfaces [GUI] specially adapted for controlling image capture or setting capture parameters
• CPC Class Codes: H04N 23/635 Region indicators; Field of view indicators
• CPC Class Codes: H04N 23/661 Transmitting camera control signals through networks, e.g. control via the Internet
• CPC Class Codes: H04N 7/18 : Closed-circuit television [CCTV] systems, i.e. systems in which the video signal is not broadcast
• CPC Class Codes: H04N 7/183 : for receiving images from a single remote source

Abstract

A data management system and method for processing, storing, and viewing the extremely large imagery data that is rapidly produced by a linear-array-based microscope slide scanner is provided. The system receives, processes, and stores imagery data produced by the linear-array-based microscope slide scanner at approximately 3 GB per minute. The data are received as a series of overlapping image stripes and combined into a seamless and contiguous baseline image. The baseline image is logically mapped into a plurality of regions that are individually addressed to facilitate viewing and manipulation of the baseline image. The data management system enables imagery data compression while scanning and capturing new image stripes. This advantageously eliminates the overhead associated with storing uncompressed image stripes. The image compression also creates intermediate level images, thereby organizing the baseline image into a variable level pyramid structure referred to as a virtual slide. The data management system efficiently converts image stripes into a high quality virtual slide that allows rapid panning and zooming by image viewing software in accordance with the individually addressed regions. The virtual slide also allows efficient processing by an algorithm framework. The data management system is costs effective and scaleable, employs standard image file formats and supports the use of virtual slides in desirable applications such as telemedicine, telepathology, microscopy education, and the analysis of high value specimens such as tissue arrays.

Claims

1. A computer implemented method for managing imagery data produced by a line scan camera, comprising:

receiving a first stripe of imagery data from a line scan camera and storing the first stripe in a buffer memory, the first stripe having a length and a width, the length being greater than the width, the first stripe having a first edge along the length and a second edge along the length;

copying a first plurality of image portions from the first stripe, each of said first plurality of image portions having an edge substantially near the first edge of the first stripe;

storing each of the first plurality of image portions as an image tile in a virtual slide image file;

receiving a second stripe of imagery data from a line scan camera and storing the second stripe in a buffer memory, the second stripe having a length and a width, the length being greater than the width, the second stripe having a first edge along the length and a second edge along the length, wherein the first edge of the second stripe overlaps the second edge of the first stripe to define a first overlap area;

aligning the second stripe with the first stripe;

copying a second plurality of image portions from the first stripe, each of said second plurality of image portions comprising a portion of imagery data from the first overlap area; and

storing each of the second plurality of image portions as an image tile in the virtual slide image file.

2. The method of claim 1, further comprising:

receiving a third stripe of imagery data from a line scan camera and storing the third stripe in a buffer memory, the third stripe having a length and a width, the length being greater than the width, the third stripe having a first edge along the length and a second edge along the length, wherein the first edge of the third stripe overlaps the second edge of the second stripe to define a second overlap area;

aligning the third stripe with the second stripe;

copying a third plurality of image portions from the second stripe, each of said third plurality of image portions having an edge adjacent to one of the second plurality of image portions; and

storing each of the third plurality of image portions from the second stripe as an image tile in the virtual slide image file.

5. The method of claim 1, wherein said aligning the second stripe with the first stripe includes:

identifying a first subset of pixels from the first stripe in the first overlap area, said first subset of pixels defining an edge of an object;

identifying a second subset of pixels from the second stripe in the first overlap area, said second subset of pixels defining an edge of an object;

comparing pixel intensities between first subset of pixels from the first stripe and the second subset of pixels from the second stripe to identify matching pattern; and

aligning the second stripe with the first stripe based on one or more identified matching pattern.

6. The method of claim 5, wherein aligning the second stripe with the first stripe includes testing a range of stripe offset values determined by a mechanical motion uncertainties from stripe to stripe.

7. The method of claim 5, further comprising:

receiving alignment information for aligning the second stripe with the first stripe; and

storing the alignment information in a stripe offset file.

3. The method of claim 3, further comprising:

copying a fourth plurality of image portions from the second stripe, each of said fourth plurality of image portions having an edge adjacent to one of the third plurality of image portions from the second stripe; and

storing each of the fourth plurality of image portions from the second stripe as an image tile in the virtual slide image file.

4. The method of claim 3, further comprising:

combining the first, second, third, and fourth plurality of image tiles into a baseline image in the virtual slide image file;

interpolating the baseline image to produce an intermediate level image having a resolution different from the baseline image;

copying a fifth plurality of image portions from the intermediate level image; and

storing each of the fifth plurality of image portions from the intermediate level image as an image tile in the virtual slide image file.

8. A system for managing imagery data produced by a line scan camera, comprising:

a first buffer memory configured to receive a first stripe of imagery data from a line scan camera, the first stripe having a length and a width, the length being greater than the width, the first stripe having a first edge along the length and a second edge along the length;

a second buffer memory configured to receive a second stripe of imagery data from a line scan camera, the second stripe having a length and a width, the length being greater than the width, the second stripe having a first edge along the length and a second edge along the length, wherein the first edge of the second stripe overlaps the second edge of the first stripe to define a first overlap area;

a processor configured to copy a first plurality of image portions from the first stripe, each of said first plurality of image portions having an edge substantially near the first edge of the first stripe, and store each of the first plurality of image portions as an image tile in a virtual slide image file, said processor further configured to align the second stripe with the first stripe, copy a second plurality of image portions from the first stripe, each of said second plurality of image portions comprising a portion of imagery data from the first overlap area, and to store each of the second plurality of image portions as an image tile in a virtual slide image file; and

a storage unit for storing the virtual slide image file.

9. The system of claim 8, wherein the processor is further configured to discard the imagery data in the first buffer memory after substantially all of the imagery data is copied into the virtual slide image file.

10. The system of claim 9, wherein in the first buffer memory is further configured to receive a third stripe of imagery data from a line scan camera, the third stripe having a length and a width, the length being greater than the width, the third stripe having a first edge along the length and a second edge along the length, wherein the first edge of the third stripe overlaps the second edge of the second stripe to define a second overlap area.

11. The system of claim 10, wherein the processor is further configured to align the third stripe with the second stripe and copy a third plurality of image portions from the second stripe, each of said third plurality of image portions having an edge adjacent to one of the second plurality of image portions from the first stripe, the processor further configured to store each of the third plurality of image portions from the second stripe as an image tile in the virtual slide image file.

12. A computer implemented method for managing imagery data produced by a line scan camera, comprising:

capturing image data through an array of sensors as a first image capture;

capturing additional image data through the array of sensors as a second image capture, wherein the second image data is adjacent to the first image data;

combining the first and second image captures in a buffer memory;

combining the first and second image captures in the buffer memory with a plurality of additional image captures, wherein each successive image capture is adjacent to the previous image capture;

copying a first plurality of image portions from the buffer memory, each of the first image portions comprising image data from a plurality of image captures;

storing each of the first plurality of image portions as an image tile in a virtual slide image file;

copying a second plurality of image portions from the buffer memory, each of the second image portions comprising image data from a plurality of image captures; and

storing each of the second plurality of image portions as an image tile in the virtual slide image file.

13. The method of claim 12, wherein the plurality of additional image captures is at least ten thousand.

14. The method of claim 12, wherein the plurality of additional image captures is at least twenty thousand.

15. The method of claim 12, wherein the plurality of additional image captures is at least thirty thousand.