Data management in a linear-array-based microscope slide scanner
Systems and methods for capturing image data using a line scan camera. In an embodiment, a line scan camera captures image data of a sample as a plurality of image stripes. A processor may coarsely align two or more of the plurality of image stripes according to a synchronization process while the line scan camera is capturing at least one of the plurality of image stripes. Subsequently, the processor may also finely align the two or more image stripes using pattern matching.
1. A system for capturing image data using a line scan camera, the system comprising:
an objective lens positioned for viewing at least a portion of a sample during constant relative motion;
a line scan camera optically coupled to the objective lens and configured to capture image data of the sample as a plurality of image stripes; and
at least one processor configured to,
while the line scan camera is capturing at least one of the plurality of image stripes of the sample, coarsely align two or more adjacent ones of the plurality of image stripes of the sample, and,
subsequently, finely align the two or more adjacent ones of the plurality of image stripes of the sample by testing a plurality of possible X-Y offset values within overlapping regions of adjacent ones of the two or more image stripes to determine an X-Y offset pair having a maximum correlation, wherein the X-Y offset pair comprises an X-Y offset for a first one of the adjacent image stripes and an X-Y offset for a second one of the adjacent image stripes.
2. The system of claim 1 , further comprising an illumination source, wherein the coarse alignment is performed according to a synchronization process that comprises:
for each of the two or more image stripes, capturing an area comprising an area preceding a predetermined scan area, the scan area, and an area following the scan area, and, during capture by the line scan camera of one or more lines of image data corresponding to a beginning of the scan area, using the illumination source to illuminate the one or more lines of image data; and,
aligning the two or more image stripes based on the illuminated one or more lines of image data in each of the two or more image stripes.
3. The system of claim 2 , wherein the at least one processor, prior to storing each of the two or more image stripes, eliminates, from each image stripe, image data corresponding to the area preceding the scan area and the area following the scan area.
4. The system of claim 2 , wherein the illuminated one or more lines of image data comprise a plurality of lines of image data.
5. The system of claim 1 , further comprising:
a position encoder that indicates a position of the sample; and
a trigger to start and stop capturing of image data by the line scan camera;
wherein coarsely aligning comprises,
when the position encoder indicates that the position of the sample corresponds to a beginning of a predetermined scan area, controlling the trigger to start capture of image data by the line scan camera, and,
when the position encoder indicates that the position of the sample corresponds to an end of the scan area, controlling the trigger to stop capture of image data by the line scan camera.
6. The system of claim 1 , wherein finely aligning further comprises selecting the plurality of possible X-Y offset values by selecting edge pixels within the overlapping regions of the adjacent image stripes.
7. The system of claim 6 , wherein selecting edge pixels within the overlapping regions of the adjacent image stripes comprises:
sorting pixels in the overlapping regions according to intensity gradient values; and
selecting a subset of the sorted pixels having highest intensity gradient values as the edge pixels.
8. The system of claim 1 , wherein the plurality of possible X-Y offset values comprise a range of X values that corresponds to a coarse alignment uncertainty representing a data latency within a synchronization process.
9. The system of claim 8 , further comprising a mechanical stage configured to move the sample relative to the objective lens, wherein the plurality of possible X-Y offset values comprise a range of Y values that corresponds to a mechanical motion uncertainty of the mechanical stage.
10. A method for capturing image data using a line scan camera, the method comprising:
by a line scan camera, capturing image data of a sample as a plurality of image stripes; and,
by at least one processor,
while the line scan camera is capturing at least one of the plurality of image stripes of the sample, coarsely aligning two or more adjacent ones of the plurality of image stripes of the sample, and,
subsequently, finely aligning the two or more adjacent ones of the plurality of image stripes of the sample by testing a plurality of possible X-Y offset values within overlapping regions of adjacent ones of the two or more image stripes to determine an X-Y offset pair having a maximum correlation, wherein the X-Y offset pair comprises an X-Y offset for a first one of the adjacent image stripes and an X-Y offset for a second one of the adjacent image stripes.
11. The method of claim 10 , wherein the coarse alignment is performed according to a synchronization process that comprises:
for each of the two or more image stripes, capturing an area comprising an area preceding a predetermined scan area, the scan area, and an area following the scan area, and, during capture by the line scan camera of one or more lines of image data corresponding to a beginning of the scan area, using an illumination source to illuminate the one or more lines of image data; and,
aligning the two or more image stripes based on the illuminated one or more lines of image data in each of the two or more image stripes.
12. The method of claim 11 , further comprising:
eliminating, from each image stripe, image data corresponding to the area preceding the scan area and the area following the scan area; and
storing each of the two or more image stripes without the eliminated image data.
13. The method of claim 11 , wherein the illuminated one or more lines of image data comprise a plurality of lines of image data.
14. The method of claim 10 , wherein the synchronization process comprises:
by a position encoder, indicating a position of the sample;
when the position encoder indicates that the position of the sample corresponds to a beginning of a predetermined scan area, controlling a trigger to start capture of image data by the line scan camera, and,
when the position encoder indicates that the position of the sample corresponds to an end of the scan area, controlling the trigger to stop capture of image data by the line scan camera.
15. The method of claim 10 , wherein finely aligning further comprises selecting the plurality of possible X-Y offset values by selecting edge pixels within the overlapping regions of the adjacent image stripes.
16. The method of claim 15 , wherein selecting edge pixels within the overlapping regions of the adjacent image stripes comprises:
sorting pixels in the overlapping regions according to intensity gradient values; and
selecting a subset of the sorted pixels having highest intensity gradient values as the edge pixels.
17. The method of claim 10 , wherein the plurality of possible X-Y offset values comprise a range of X values that corresponds to a coarse alignment uncertainty representing a data latency within a synchronization process.
18. The method of claim 17 , wherein the plurality of possible X-Y offset values comprise a range of Y values that corresponds to a mechanical motion uncertainty of a mechanical stage configured to move the sample.