PrePATH: A Toolkit for Preprocessing Whole Slide Images

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PrePATH is a comprehensive preprocessing toolkit for whole slide images (WSI), built upon CLAM and ASlide.

TODO

• H0-mini
• OpenMidnight
• TITAN (Slide level)

Installation

Prerequisites

• Anaconda or Miniconda
• openslide-tools (system dependency)

Setup Instructions

The following instructions demonstrate installation for the GPFM model. For other foundation models, please refer to their respective repositories for environment-specific requirements.

git clone https://github.com/birkhoffkiki/PrePATH.git
cd PrePATH
conda create --name gpfm python=3.10
conda activate gpfm
pip install -r requirements/gpfm.txt
cd models/ckpts/
wget https://github.com/birkhoffkiki/GPFM/releases/download/ckpt/GPFM.pth

Notes:

• ASlide should be installed as a Python package from GitHub and is included in requirements/gpfm.txt.
• Environment configurations for other foundation models should be referenced from their respective repositories.

Usage

Step 1: Patch Coordinate Extraction

Extract coordinates of foreground patches from whole slide images:

# Configure variables in the script before execution
bash scripts/get_coors/SAL/sal.sh

Step 2: Feature Extraction

Extract patch-level features using the selected foundation model:

# Refer to the script for detailed configuration options
bash scripts/extract_feature/sal.sh

Supported Foundation Models

PrePATH supports multiple state-of-the-art foundation models for patch-level feature extraction. To extract features using specific models (e.g., ResNet50 and GPFM), configure the models parameter in scripts/extract_feature/exe.sh:

models="resnet50 gpfm"

Note: Each foundation model requires its corresponding Python environment to be properly configured.

Model	Identifier	Reference
ResNet50	resnet50	Standard ImageNet pretrained model
GPFM	gpfm	GitHub
CTransPath	ctranspath	GitHub
PLIP	plip	GitHub
CONCH	conch	HuggingFace
CONCH-1.5	conch15	HuggingFace
UNI	uni	HuggingFace
UNI-2	uni2	HuggingFace
mSTAR	mstar	GitHub
Phikon	phikon	HuggingFace
Phikon2	phikon2	HuggingFace
Virchow-2	virchow2	HuggingFace
Prov-GigaPath	gigapath	HuggingFace
CHIEF	chief	GitHub
H-Optimus-0	h-optimus-0	HuggingFace
H0-mini	h0-mini	HuggingFace
H-Optimus-1	h-optimus-1	HuggingFace
OpenMidnight	openmidnight	HuggingFace
Lunit	lunit	GitHub
Hibou-L	hibou-l	GitHub
MUSK	musk	HuggingFace
OmiCLIP	omiclip	Github
PathoCLIP	pathoclip	Github

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Supported WSI Formats

PrePATH supports the following whole slide image formats:

• KFB (.kfb)
• SDPC (.sdpc)
• TRON (.tron)
• All formats supported by OpenSlide (including .svs, .tiff, .ndpi, .vms, .vmu, .scn, .mrxs, .tif, .bif, and others)