JPWO2021250373A5

JPWO2021250373A5 -

Info

Publication number: JPWO2021250373A5
Application number: JP2022573304A
Authority: JP
Publication date: 2024-05-24

Claims

1. A method of operating a microscope scanner having a detector array, comprising:
performing a pre-scan to generate a pre-scan image of a target, the target comprising a sample, the pre-scan having a depth of focus for the pre-scan exceeding 500 micrometers;
performing automated image analysis of the pre-scan image to generate a first probability map indicating where on the target the sample is expected to be present;
performing a first imaging scan of one or more areas of interest (AOI) on the target , the one or more AOIs being selected from the first probability map;
moving the detector array relative to the target along an image scan path and acquiring an image of the target using the detector array at each of a plurality of locations along the image scan path, wherein the depth of focus for each image acquired during the first imaging scan is less than 3 micrometers;
generating focus control data during the imaging scan, said generating comprising calculating a focus merit value at each of the locations along the image scan path ;
adjusting a focal height of the detector array along the image scan path based on the focus merit value; and
combining images of the target acquired at each of the plurality of locations along the image scan path to form a first image of the target;
performing the first imaging scan comprising:
analyzing the effectiveness of the first imaging scan using the focus control data, and determining changes to one or more scanning parameters from the first imaging scan for performance of a second imaging scan based on the analysis;
23. A method comprising:

the first imaging scan is performed across a first scan area comprising the one or more AOIs;
The method of claim 1 , wherein determining to alter one or more scan parameters comprises selecting a second scan area on the target that is different from the first scan area.

analyzing the validity of the first imaging scan comprises identifying one or more boundary locations on the target where the focus control data indicates that the detector array was in focus at a boundary of the first scan area;
3. The method of claim 2, wherein selecting the second scan area comprises adjusting the first scan area to incorporate an area of the target outside the first scan area surrounding the one or more boundary locations.

analyzing the effectiveness of the first imaging scan comprises identifying one or more sample focal regions on the target from the focus control data indicating that the detector array was in focus throughout the one or more sample focal regions;
3. The method of claim 2, wherein selecting the second scan region comprises interpolating an area of the target through which the sample extends outside the one or more sample focal regions imaged during the first imaging scan.

The method of claim 4, wherein the shape of the interpolated region is found by applying a shape fit to the contour of the sample focal region.

evaluating the validity of the first imaging scan further comprises identifying one or more poor focus regions on the target, the focus control data indicating that the detector array was out of focus throughout the one or more poor focus regions during the first imaging scan;
6. The method of claim 2, wherein determining a change to the one or more scanning parameters comprises adjusting a focusing procedure to obtain images of the target at a different focus height during the second imaging scan in the one or more poor focus regions compared to corresponding images from the first imaging scan.

evaluating the validity of the first imaging scan further comprises identifying one or more poor focus regions on the target, the focus control data indicating that the detector array was out of focus throughout the one or more poor focus regions during the first imaging scan;
2. The method of claim 1, wherein determining a change to the one or more scanning parameters comprises adjusting a focusing procedure to obtain an image of the target at a different focus height during the second imaging scan in the one or more poor focus regions compared to corresponding images from the first imaging scan .

The first imaging scan further comprises deriving a second image of the target from the first image, the second image having a lower resolution than the first image;
The step of analyzing the validity of the first imaging scan includes:
performing automated image analysis of the second image to generate a second probability map for areas of the target where the sample is expected to be present;
identifying surface details in the pre-scan image that correspond to locations on the target where the first probability map indicates that the sample is expected to be present and the second probability map indicates that the sample is not present;
Further comprising:
The method of claim 7 , wherein the one or more poor focus regions exclude locations on the target having the surface detail.

The method of claim 8, wherein the resolution of the second image is approximately equal to the resolution of the pre-scan image.

the focus control data comprises an estimated focal plane of the target at each location along the image scan path, and an actual focal height of the detector array is monitored for each location along the image scan path at which an image is acquired;
10. The method of claim 7, wherein identifying one or more poor focus regions on the target comprises identifying one or more position error locations where a difference between the estimated focal plane and the actual focal height of the detector array exceeds an error threshold.

the first imaging scan further comprises generating a first image of the target from the images acquired along the image scan path;
A method according to any one of claims 7 to 9, wherein the step of identifying one or more poor focus regions further comprises the steps of performing an automated image analysis of one or more subregions of the first image to identify whether the focus of the first image is acceptable, and designating each subregion of the target in which the focus is unacceptable as a poor focus region, the one or more subregions being selected based on the focus control data.

The method of claim 11 , wherein the one or more sub-regions include position error locations.

The method of any one of claims 7 to 9, further comprising, prior to the first imaging scan, measuring a focus position for at least one seed location within the one or more AOIs , and setting the focus height at one or more locations along the image scan path based on the measured focus position for the seed location.

The method of claim 13, wherein the one or more scanning parameters are selected from the group including an area of the target imaged, a number of seed locations on the target, and a location of the seed locations on the target.

The method of claim 13 , wherein analyzing the validity of the first imaging scan comprises identifying an error in the measured focus position relative to one or more of the seed locations.

The method of claim 15, wherein identifying the error in the focus position comprises comparing the focus control data from the first imaging scan to the measured focus position for the one or more seed locations prior to the first imaging scan.

17. The method of claim 16, wherein comparing the focus control data from the first imaging scan to the measured focus positions for the one or more seed locations prior to the first imaging scan comprises comparing the focus control data from the seed locations during the first imaging scan to the measured focus positions for the one or more seed locations prior to the first imaging scan.

14. The method of claim 13, wherein determining a change in one or more scan parameters from the first imaging scan comprises selecting a new seed location on the target at a location where the focus control data indicates that the detector array was out of focus during the first imaging scan.

the first imaging scan is performed across a plurality of AOIs, and the focus position is measured by adjusting the focal height of the detector array through a range of positions perpendicular to a face of the target at each of the seed locations;
analyzing the effectiveness of the first imaging scan comprises calculating an average focus height of the samples within each of the plurality of AOIs from the focus control data;
14. The method of claim 13, wherein in response to finding a separation between average focus heights for a first AOI and a second AOI of the plurality of AOIs exceeding a threshold distance, determining a change to one or more scan parameters from the first imaging scan comprises modifying a range of positions over which the focus height is adjusted when monitoring the focus position at the seed location within the first AOI to exclude the average focus height for the first AOI calculated from the first imaging scan, wherein the average focus height calculated for the first AOI exceeds the average focus height calculated for the second AOI.

20. The method of claim 19, wherein the average focus height calculated for the second AOI is the lowest focus height from a group that includes the average focus heights calculated for each of the multiple AOIs.

14. The method of claim 13, further comprising performing the second imaging scan of the target using the detector array with the determined changes in the one or more scanning parameters relative to the first imaging scan performed.

13. A computer program product containing instructions that when executed using a microscope scanner comprising a detector array and a target comprising a sample causes the microscope scanner to perform the method of claim 1 .