PathoImage Toolkit
Standalone desktop utility for digital pathology and microscopy image workflows, including whole-slide image preview, ROI cropping, tiling, reconstruction, downsampling, OME-TIFF handling, Leica LIF support and metadata-aware processing.
Overview
PathoImage Toolkit is the evolution and rebranding of TiffCropper, expanding the original crop, tile and merge functionality into a broader utility for digital pathology and microscopy image workflows. It supports large-image visualization, ROI extraction, image splitting, reconstruction, metadata preservation and format-aware processing in research settings.
The application is suited to whole-slide images, microscopy datasets, OME-TIFF files and large multichannel resources where preserving spatial calibration and image metadata is important for downstream analysis.
Key features
- Whole-slide and large microscopy image visualization and preview
- Coordinate-based ROI cropping
- Fixed-size tiling and row/column image division
- Tile reconstruction and image merging
- Image downsampling
- Multichannel image support and channel visualization
- OME-TIFF metadata and spatial calibration preservation
- Leica LIF image splitting and conversion
- GeoJSON annotation visualization and editing
- BigTIFF-compatible workflows for large outputs
Quick start
- Open the application and select a supported image file.
- Use the preview to inspect the image and target region.
- Choose the required workflow: crop, tile, merge, downsample or another available utility.
- Configure output settings and destination folder.
- Run the process and review the generated outputs.
Typical use cases
- Extract high-resolution ROIs from whole-slide images
- Prepare tiles for machine learning or quantitative image analysis
- Reconstruct images after tile-based processing
- Preserve microscopy calibration metadata in derived outputs
- Split, convert and organize large pathology or microscopy image files
Project transition
PathoImage Toolkit is the continuation of the project previously distributed as TiffCropper. The new name reflects the expansion from a focused crop/tile utility into a broader pathology and microscopy toolkit.
Previous release
TiffCropper v1.2
DOI: 10.5281/zenodo.20316535
Current release
PathoImage Toolkit v2.0
DOI: 10.5281/zenodo.21956932
Supported workflows
- TIFF / pyramidal TIFF / BigTIFF
- OME-TIFF
- Whole-slide formats through available readers
- Leica LIF
- JPEG and PNG
- GeoJSON annotation workflows
Screenshot
Visualization of the PathoImage Toolkit interface.
