Systems and methods for automated analysis of cells and tissues

A method implemented by computer to locate and quantify a particular biomarker in tissue samples containing cells, and the method comprises: a) using an optical imaging device to obtain: i) a first image of a cell with a first staining that is selective for a first defined area within the cell; ii) a second image of the cell with a second stain that is selective for a biomarker; and iii) a third image of the cell with a third staining that is selective for a second defined area within the cell, in which each image is composed of pixel locations; b) read the pixel intensity at each pixel location of the first image and the third image and compare each intensity value with a predetermined threshold intensity value; c) assign each pixel location in the first image and the third image to the first defined area, the second defined area, or a third defined area, in which, for each pixel location, if the pixel intensity value in the pixel location only in the first image is greater than the respective threshold intensity value, the pixel location is assigned to the first defined area, if the pixel intensity value at the pixel location only in the third image is greater than the respective threshold intensity value, the pixel location is assigned to the second defined area, if the pixel intensity values ​​at the location of Pixel both in the first image and in the third image are below the respective threshold intensity values, the pixel location is assigned to the third defined area, and if the pixel intensity values ​​at the pixel location in both the first image and the third image are greater than the respective threshold intensity values, the pixel intensity values ​​are compared and the pixel location is assigned to the defined area that corresponds to the image that has the highest pixel intensity value at the pixel location; d) determine the amount of intensity of the first defined area incorrectly assigned to the second defined area and the amount of intensity of the second area defined incorrectly assigned to the first defined area and reallocate the pixel locations to the first defined or second area defined area with respect to a weighted intensity ratio of the first defined area with respect to the second defined area, and the weighting is determined by a factor that is increased iteratively until the amount of incorrectly assigned pixel locations is less than 5%; e) compare the second image with the first and third images to identify the pixel locations in the second image that are within the first defined area or the second defined area; and f) add the intensity values ​​of the pixel locations in the second image assigned to similar defined areas to locate and thus quantify the biomarker in tissue samples containing cells.