Method for detecting immunostaining below the threshold of visual perception

A method comprising:

• obtaining a patient's at least one first and at least one second tissue sections;
• using a biomarker staining process to stain the at least one first tissue sections for biomarker expression to generate at least one stained tissue section;
• using a control staining process to stain the at least one second tissue sections with a control to generate at least one control tissue section;
• obtaining at least one digital image of the at least one stained tissue sections and at least one digital image of the at least one control tissue sections;
• modifying an algorithm process until the algorithm process produces data from the at least one digital image of the control tissue section that recapitulates an orthogonal biomarker expression dataset to generate a threshold;
• applying the threshold to the modified algorithm process to generate an analysis algorithm process;
• extracting a first dataset that associates a quantity of the biomarker at a specific location in a tissue object in the stained tissue section from the control tissue section by applying the analysis algorithm process to the at least one digital image of the control tissue section;
• extracting a second dataset that associates a quantity of the biomarker at a specific location in a tissue object in the stained tissue section from the stained tissue section by applying the analysis algorithm process to the at least one digital image of the stained tissue section;
• calculating a patient-specific biomarker score from the first and second datasets, wherein the patient-specific biomarker score cannot be generated by visual assessment of the stained tissue sample;
• and
• determining at least one patient status for the patient based on the patient-specific biomarker score, wherein the at least one patient status is selected from the group consisting of diagnosis, disease severity, disease progression, therapy candidacy, and therapy efficacy.