Automated methods and systems for detecting cells in stained specimen images

An image analysis system comprising one or more processors and coupled to at least one memory storing instructions which, when executed by the one or more processors, cause the tissue analysis system to perform the operations of:

• deconvolving a specimen image into at least a first information channel and a second information channel;
• generating a stain image along the first information channel;
• generating a counter stain image along the second information channel;
• generating a complement of the stain image;
• process the complement of the stain image using a segmentation operation to generate a first segmented nuclei image, wherein the first segmented nuclei image indicates a first set of image objects in the specimen image that correspond to a first set of nuclei;
• process the counter stain image using the segmentation operation to generate a second segmented nuclei image, wherein the second segmented nuclei image indicates a second set of image objects in the specimen that correspond to a second set of nuclei;
• and
• combining the first and second segmented nuclei images to generate a combined segmented nuclei image, wherein the combined segment nuclei image indicates bot the first and second set of image objects.

A non-transitory computer-readable medium including instructions which, when executed by one or more processors of an image analysis system, cause the image analysis system to perform a plurality of operations for detecting nuclei in a specimen image, the operations comprising:

• deconvolving the specimen image into at least a first information channel and a second information channel;
• generating a stain image along the first information channel;
• generating a complement of the stain image;
• generating a counter stain image along the second information channel;
• combining the complement of the stain image and the counter stain image to generate a combined image;
• processing the combined image using a segmentation operation to detect a plurality of image objects in the combined image, each of the plurality of image objects corresponding to a cell nucleus of the specimen;
• and
• outputting the combined image with the detected plurality of image objects.