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

IHC Dataset CSV

Documentation Source

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

Windows TIFF ROI

Documentation Source

iSyntaxToTIFF

Standalone converter for Philips .isyntax whole-slide images to pyramidal RGB OME-TIFF, using OpenPhi and the Philips Pathology SDK.

Philips .isyntax to pyramidal RGB .ome.tif
SDK setup and SDK import test from the GUI
Batch conversion with CSV conversion log

iSyntax OME-TIFF Converter

Documentation Source

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

Registration DeeperHistReg GUI

Documentation Source

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

IF microscopy Segmentation Manders

Documentation Source

FeatureStat Studio

Desktop GUI for grouped statistical analysis, publication-ready plots, histograms, ROC biomarker evaluation and multi-feature batch visualization.

Grouped statistics and publication-ready plots
Histogram and ROC biomarker analysis
Multi-feature batch preview and export

Statistics ROC Features

Documentation Source

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

QuPath GeoJSON Annotations

Documentation Source

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.