Generating annotation data of tissue images

A computer-implemented medical image annotation method for automatically generating annotation data of tissue images comprising:

• receiving first image data comprising a representation of a tissue sample stained with a first stain for indicating tissue structure;
• receiving second image data comprising a representation of the tissue sample stained with a second stain for revealing the presence of a biomarker in the tissue sample;
• detecting a plurality of candidate objects in the first image data, and a corresponding plurality of detection probabilities of the detected candidate objects;
• generating stain confidence data of the second image data representing a likelihood that a corresponding portion of the tissue sample comprises the biomarker targeted by the second stain, comprising segmenting the plurality of candidate objects in the first image data, transferring the segmentation of the plurality of candidate objects in the first image data to the second image data based on the registration between the first and second image data, and summing the corresponding stain confidence data in the location of the plurality of candidate objects in the second image data, wherein the summed stain confidence data is used with the plurality of detection probabilities of the detected candidate objects to determine a likelihood score value for candidate objects to be positive for the biomarker targeted by the second stain;
• and
• generating image annotation data comprising a representation of the plurality of candidate objects, wherein the individual candidate objects of the plurality of candidate objects are annotated to indicate biomarker presence in corresponding portions of the second image data if an individual candidate object reaches a combined confidence based on the corresponding plurality of detection probabilities of the detected candidate objects, the corresponding stain confidence data, and a corresponding registration quality threshold of a registration between the first and second image data of the candidate objects, and wherein generating the image annotation data comprises generating a registration quality map between the first image data and the second image data, and only annotating candidate objects of the plurality of candidate objects to indicate biomarker presence when the registration quality map indicates that the registration between corresponding locations of the candidate object in the first and second image data surpasses a registration quality threshold.

A method for generating annotation data of tissue images comprising:

• segmenting a plurality of candidate objects in first image data, wherein the first image data comprises a representation of a tissue sample stained with a first stain for indicating tissue structure;
• transferring the segmentation to second image data based on a registration between the first and second image data, wherein the second image data comprises a representation of the tissue sample stained with a second stain for revealing the presence of a biomarker in the tissue sample;
• summing corresponding stain confidence data in the location of the plurality of candidate objects in the second image data, wherein the summed stain confidence data is useable with a plurality of detection probabilities of detected candidate objects to determine a likelihood score value for candidate objects to be positive for the biomarker targeted by the second stain;
• and
• generating a registration quality map between the first image data and the second image data, wherein candidate objects of the plurality of candidate objects are annotated to indicate biomarker presence depending on whether the registration quality map indicates that the registration between corresponding locations of the candidate object in the first and second image data surpasses a registration quality threshold.