Changelog

All notable changes to this project will be documented in this file.

[0.1.0] - 2025-01-29

Added

  • Patch extraction from whole slide images

  • Multiple cell segmentation models: - CellViT: Vision transformer-based nuclear instance segmentation - HoverNet: Nuclear instance segmentation - Cellpose: Deep learning cell instance segmentation

  • Feature extraction capabilities: - PyRadiomics_Gray: Comprehensive radiomics features - PyRadiomics_HED: Comprehensive radiomics features - Morphometrics: Morphological features

  • Multiple Instance Learning models: - CLAM: Clustering-constrained attention MIL - TransMIL: Transformer-based MIL with PPEG - Standard MIL: Max pooling MIL - HistoBistro: Transformer-based MIL

  • Command-line interface for all operations

  • Feature visualization tools

  • Graph creation tools

  • Dataset creation and management

  • Model training and evaluation pipelines

Features

  • Support for multiple WSI formats (SVS, TIFF, NDPI, etc.)

  • GPU acceleration for deep learning models

  • Configurable patch extraction parameters

  • Comprehensive logging and error handling

  • Type-safe configuration with Pydantic