CD3, Lymphocytic Colitis CD3, Lymphocytic Colitis

Process APP




CD3, Lymphocytic Colitis

Microscopic colitis is a type of inflammation of the colon that causes non-bloody watery diarrhea and most often impacts middle-aged females. The condition can be distinguished into two types, lymphocytic and collagenous. The difference between the two types are minor; both are characterized by an increase in lymphocytes with collagenous colitis also having a thickened subepithelial collagen layer.
This APP is addressing lymphocytic colitis.

By quantifying the T-lymphocytes targeted by the CD3 marker in different tissue compartments, a diagnosis can be determined.

Figure 1

Figure 1

The auxiliary APP “01 ROI detect” automatically outlines the relevant tissue on slide.

Figure 2

Figure 2

Next the intestinal glands and the tissue border is detected. The intestinal glands are marked with a red ROI, while the tissue border is marked with a blue ROI.

Figure 3

Figure 3

Close up of detected intestinal glands and the tissue border.

Figure 4

Figure 4

Final analysis result: CD3 positive (red) and CD3 negative tissue (blue) is identified. The APP outputs the percentage of CD3 positive area within each compartment, i.e. the intestinal glands and the tissue border. The APP also outputs the overall CD3 positive area on the slide.


Auxiliary APPs

ROI detect:

APP: “01 ROI detect”
This APP can be used for automatic and precise detection of tissue present in the image, thereby limiting the analysis to only occur within relevant tissue areas and not on the entire image.

Quantitative Output variables

The output variables obtained from this protocol are:

  • % Positive (Tissue): The CD3 positive percentage in all tissue (area based calculation).
  • % Positive (Border): The CD3 positive percentage in the tissue border (area based calculation).
  • % Positive (Islets): The CD3 positive percentage in the intestinal glands (area based calculation).


The APP detects the tissue regions and separates the intestinal glands and tissue border from the remaining tissue via edge detection based on Hematoxylin deconvolution. The brown CD3 positive stained and blue negative stained areas are then quantified and calculated within the three tissue regions.

Staining Protocol

There is no staining protocol available.


Colon, colorectal, colitis, CD3, lymphocytic, collagenous, human, digital pathology, image analysis, quantitative.


There are no references available.

Your message has been successfully sent!