Tools
A collection of software tools designed to support scalable digital pathology workflows, from whole-slide image processing to dataset preparation and quantitative analysis.
HPA Image Downloader
Automated downloader for IHC cancer images from the Human Protein Atlas, generating structured folders and CSV metadata summaries for dataset construction.
- Batch IHC image retrieval
- Structured dataset organization
- CSV metadata export
TiffCropper
Standalone Windows application for extracting high-resolution ROIs from large TIFF microscopy images, preserving calibration metadata and spatial integrity.
- Handles large TIFF / WSI-like images
- Metadata-safe cropping
- Designed for reproducible ROI workflows
HistRegGUI
Desktop GUI for histology image registration using DeeperHistReg presets (initial, rigid, nonrigid) with CPU-only execution support.
- Multi-stage registration pipeline
- CPU-friendly execution
- Designed for section alignment & 3D reconstruction workflows
Pipeline Development
Beyond standalone tools, current development focuses on an end-to-end WSI processing pipeline that transforms raw whole-slide images into structured, analysis-ready datasets.
The system integrates automated tissue detection, artifact cleaning, efficient patch extraction and storage, and segmentation modules for quantitative tumor microenvironment (TME) characterization.