Methods and systems for processing images of three-dimensional biological samples

A method for analyzing a plurality of three-dimensional samples positioned in a plurality of microwells, the method comprising:

• obtaining a first image of the plurality of microwells;
• applying a first image processing step to the first image of the plurality of microwells to identify a geometry of each of the plurality of microwells, wherein the first image processing step creates a second image of the plurality of microwells;
• applying a second image processing step to the second image of the plurality of microwells to generate a first mask of each of the plurality of microwells, wherein the second image processing step creates a third image of the plurality of microwells;
• applying a third image processing step to the first image of the plurality of microwells to generate a second mask to detect walls of the plurality of microwells, wherein the third image processing step creates a fourth image of the plurality of microwells;
• preparing an intersection of the second image and the fourth image to create a fifth image of the plurality of microwells that removes the detected walls of each of the plurality of microwells;
• preparing a union of the third image and the fifth image to create a sixth image of the plurality of microwells that includes a location of the plurality of three-dimensional samples inside each of the plurality of microwells;
• applying the sixth image as a filter to the first image of the plurality of three-dimensional samples to generate a seventh image;
• and
• identifying the plurality of three-dimensional samples positioned in the plurality of microwells from the seventh image.