PathoImage Toolkit is the evolution and rebranding of TiffCropper, expanding the original WSI crop, tile, and merge functionality into a broader desktop utility for digital pathology and microscopy image workflows.
This release represents a major evolution of the project, with expanded support for whole-slide images, multichannel microscopy data, OME-TIFF metadata, Leica LIF files, annotations, image visualization, and large-image processing.
Highlights
Whole-slide image workflows
- Whole Slide Image (WSI) visualization and preview
- Interactive ROI cropping
- Fixed-size tiling
- Row/column-based image division
- Tile reconstruction and image merging
- Image downsampling
- Improved handling of very large images and memory-intensive workflows
Microscopy and multichannel imaging
- Multichannel image support
- Channel visualization and preview controls
- Support for fluorescence and microscopy image workflows
- Leica LIF image splitting and conversion
OME-TIFF and metadata
- OME-TIFF support
- Preservation of spatial calibration and pixel-size metadata when available
- Improved handling of image metadata during crop, tile, merge, and downsampling operations
- Support for pyramidal TIFF workflows
Annotation workflows
- GeoJSON annotation loading and visualization
- Annotation editing and export
- Integration of annotations with image preview and ROI workflows
Image format support
PathoImage Toolkit supports multiple digital pathology and microscopy image formats, including:
- TIFF / pyramidal TIFF
- OME-TIFF
- SVS
- NDPI
- MRXS
- Leica LIF
- JPEG
- PNG
- Additional formats supported through the available image-reading backends
Project transition
Previous releases of this project were distributed as TiffCropper.
The original software focused primarily on WSI cropping, tiling, and reconstruction. As the application expanded to include microscopy, multichannel imaging, OME-TIFF processing, Leica LIF conversion, GeoJSON annotations, metadata preservation, and additional image-processing utilities, the project was renamed PathoImage Toolkit to better reflect its broader scope.
Previous release
TiffCropper v1.2
The historical TiffCropper release remains permanently archived on Zenodo under its original name and DOI.
Current release
PathoImage Toolkit v2.0
Starting with this release, the project is distributed and maintained as PathoImage Toolkit.
Repository
https://github.com/Juaco2r/PathoImage-Toolkit
License
MIT License
Author
José Rodriguez-Rojas