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INSTALL.md

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Installation Guide for NePathTK

This document provides instructions to set up NePathTK (NephroPathology Toolkit), including environment preparation and configuration of required files.

1. Prerequisites

2. Clone the Repository

git clone https://github.com/Nicolik/NePathTK.git
cd NePathTK

3. Python Environment Setup

We recommend creating a new environment:

conda create -n nepathtk python=3.7.16 -y
conda activate nepathtk

Then install required dependencies:

pip install numpy cached-property
pip install torch==1.13.1 torchvision==0.14.1 --index-url https://download.pytorch.org/whl/cu117
pip install -r requirements.txt

Install mmsegmentation dependencies:

pip install -U openmim
mim install mmengine
mim install "mmcv==2.0.0"
pip install "mmsegmentation>=1.0.0"
mim install mmdet
pip install ftfy

4. Configuration Files

After installation, some .base configuration files must be adapted to your local setup:

4.1 definitions.py

  • Copy from the provided base file:
cp definitions.py.base definitions.py
  • Edit definitions.py and provide valid paths for:
    • DATASET_DIR → directory where the classification dataset is stored
    • OPENSLIDE → directory containing OpenSlide binaries (needed for smooth integration with openslide-python)

4.2 config_semseg.py

  • Copy from the base file:
cp config_semseg.py.base config_semseg.py
  • Edit config_semseg.py and define the class SelectedConfig, including the paths.

4.3 .paquo.toml

  • Copy from the base file:
cp .paquo.toml.base .paquo.toml
  • Edit .paquo.toml and set the path to your QuPath executable.

5. Verification

  1. Check that all three files exist and are configured:

    • definitions.py
    • config_semseg.py
    • .paquo.toml

  2. You can also verify that everything went smoothly with the install_check script:

python install_check.py"

✅ Installation Complete

You are now ready to use NePathTK for multistain multicompartment segmentation and classification workflows in nephropathology.

For details on usage, please refer to the project documentation and examples.