Systems and methods for automated analysis of cells and tissues

A method of analyzing a cell containing sample, comprising:

• obtaining a first image of a cell with a first stain that is selective for a first defined area within the cell and a second stain that is selective for at least one biomarker;
• determining an intensity value for the first stain at a plurality of pixel locations in the first image;
• based on the intensity values, determining pixel locations in the first image that correspond to the first defined area within the cell and assigning those pixel locations to the first defined area;
• obtaining a second image and determining an intensity value for the second stain at a plurality of pixel locations in the second image;
• and
• comparing the first and second images to identify pixel locations in the second image that are within the first cellular compartment.

A method of analyzing a cell containing sample, comprising:

• accessing a value for each of a plurality of pixel locations in a first image of a cell;
• accessing a value for each of the plurality of pixel locations in a second image of a cell;
• and
• subtracting a percentage of the intensity value for each pixel location in the second image from the intensity value of the same pixel location in the first image to obtain an adjusted intensity value.

A method of analyzing a plurality of spots, comprising:

• locating the spots;
• defining a reference point for the located spot;
• connecting the reference point of the located spot to the reference point of a set of nearest neighbor spots with a corresponding line segment;
• and
• identifying points of intersection between line segments used to connect spots to each other.