CAPPER

CAPPER (Capillary / Pericyte Quantification Tool) is a Python-based image analysis tool designed for automatic quantification of capillary density and pericyte coverage in microscopy images.

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Abstract

The vascular system ensures sufficient blood supply and tissue homeostasis and consists of different cell types. Endothelial cells represent the structural backbone of blood vessels and are accompanied by murals cells, specifically pericytes in the microcirculation as well as vascular smooth muscle cells (vSMC) along the larger vessels (arteries, arterioles and veins). Distinguishing these different cell types in immunohistochemical stainings presents a challenge due to their close proximity and the unreliable marker distribution of mural cells. Furthermore, manual quantification of capillaries and pericytes is highly examiner-dependent, hindering inter-examiner and inter-laboratory comparisons. To address these issues, we developed an automated algorithm-based analysis software designed to standardize quantification of vascular structures in immunohistochemical images, named CAPPER (Capillary / Pericyte Quantification Tool). Through the implementation of adaptive thresholding, morphological operations, and domain-specific knowledge, CAPPER excels in the quantification of capillary densities and pericyte coverage in different organs (brain, heart, muscle, and kidney), species (mouse and pig) as well as a plethora of disease states.

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Installation

1. Clone the repository

git clone https://github.com/ariogato/capper.git
cd capper

2. (Optional) Create a virtual environment

python3 -m venv venv
source venv/bin/activate  # On macOS/Linux
venv\Scripts\activate     # On Windows

3. Install dependencies

pip install -r requirements.txt

Usage

1. Run the main script

python main.py

2. Select a Folder

When the program starts, a file dialog will open. Choose a directory that contains .tif or .tiff files. The main window will then display all TIFF files in the folder.

3. Create Groups

To create a group:

1. Select one or multiple TIFF files from the left list
2. Enter a group name in the input field on the right
3. Click “Create Group”

The group will appear in the right panel.

4. View Groups

On the right side, you will see:

• Group names
• Number of files per group
• Files inside each group

5. Run Processing

When you are done grouping:

Click the RUN button. When the algorithm is done, the result will appear in a newly created output directory.