A Fiji plugin package providing tools for BigDataViewer, including image fusion, GPU-accelerated deconvolution, registration, and data processing. Developed by BIOP (BioImaging and Optics Platform) at EPFL.
- Multi-format support: Open CZI (Zeiss), LIF (Leica), Operetta (PerkinElmer), Imaris (.ims), and standard ImagePlus
- Zeiss LLS7: Live deskewing for lattice light-sheet data
- BigStitcher integration: Convert and fuse BigStitcher datasets to OME-TIFF
- Warpy workflow: Interactive registration for QuPath projects with landmark-based alignment
- Automated registration: SIFT and Elastix-based affine and B-spline registration
- Multiscale registration: Coarse-to-fine registration across resolution levels
- GPU Deconvolution: Lazy, tiled Richardson-Lucy deconvolution using CLIJ2 (see Deconvolution README)
- Alpha blending: Layer-based compositing with multiple blending modes
- Source fusion: Block-based fusion with bounded cache for large datasets
- 3D transforms: Rotation, recentering, Z-offset removal
- Elliptical projection: Spherical/ellipsoidal coordinate transforms for curved surfaces
- Oblique slicing: Resample sources along arbitrary view orientations
Enable the PTBIOP update site in Fiji:
Help > Update... > Manage Update Sites- Check PTBIOP
- Close and restart Fiji
Commands appear under Plugins > BigDataViewer > BigDataViewer-Playground.
This package builds on:
- bigdataviewer-playground - Core BDV infrastructure
- bigdataviewer-core - BigDataViewer library
- CLIJ2 - GPU acceleration (OpenCL)
- QuPath - Warpy registration workflow integration
- BigStitcher - Tile stitching and fusion
- Elastix - Deformable image registration