Tools
A collection of software tools designed to support scalable digital pathology workflows, from whole-slide image processing to dataset preparation, image registration, segmentation, annotation conversion 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
PathoImage Toolkit
Desktop utility for digital pathology and microscopy image workflows, including large-image visualization, ROI cropping, tiling, reconstruction, downsampling, OME-TIFF handling, Leica LIF conversion and annotation-aware tools.
- WSI preview, ROI cropping, tiling and reconstruction
- OME-TIFF metadata and spatial calibration preservation
- Multichannel, Leica LIF and GeoJSON-aware workflows
HistoAnnotator
Cross-platform histology and microscopy annotation application for Web, Windows, Linux, macOS and Android, with whole-slide viewing, QuPath-compatible GeoJSON, local workflows, Desktop server pairing and multichannel fluorescence visualization.
- Interactive WSI and microscopy annotation tools
- Standalone Desktop builds for Windows, Linux and macOS
- Android local image support and QR-based Desktop pairing
- QuPath-compatible GeoJSON import and export
HistoAnalyzer
Cross-platform desktop application for reproducible H-DAB histology analysis, integrating tissue classification, anthracosis detection, nuclei segmentation, compartment prediction and DAB quantification.
- H-DAB tissue and artifact-aware analysis pipeline
- Tumor / Stroma / Other compartment workflows
- GeoJSON, CSV, TIFF and QC image outputs
iSyntaxToTIFF
Standalone converter for Philips .isyntax whole-slide images to pyramidal RGB OME-TIFF,
using OpenPhi and the Philips Pathology SDK.
- Philips
.isyntaxto pyramidal RGB.ome.tif - SDK setup and SDK import test from the GUI
- Batch conversion with CSV conversion log
HistRegGUI
Desktop GUI for histology image registration using DeeperHistReg presets with CPU-only execution support.
- Multi-stage registration pipeline
- CPU-friendly execution
- Designed for section alignment & 3D reconstruction workflows
Cell Well Segmentation
Desktop GUI for immunofluorescence cell segmentation, feature extraction, Manders colocalization analysis, QuPath-compatible GeoJSON export and optional DICE validation using ground-truth annotations.
- ROI-based parameter exploration
- Instance mask, CSV, Manders and GeoJSON outputs
- DICE/IoU validation against full-image GeoJSON annotations
FeatureStat Studio
Desktop GUI for rapid grouped statistical exploration, quick data visualization, histograms, ROC biomarker evaluation and multi-feature batch analysis.
- Grouped statistics and rapid exploratory plots
- Histogram and ROC biomarker analysis
- Multi-feature batch preview and export
QuPath GeoJSON Converter
Desktop GUI for converting external GeoJSON annotations into QuPath-compatible annotations, detections and class-based objects.
- GeoJSON classification conversion
- Annotation, detection and object-count modes
- Batch file and folder processing
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 characterization.