Olivier Burri, Romain Guiet, Arne Seitz
BioImaging & Optics Platform (BIOP)
Ecole Polytechnique Fédérale de Lausanne
This ActionBar provides simple access to our Olympus Slide Scanner .VSI Files. Includes tools for extracting and resizing whole tissue scans.
Fast tiling microscopes are becoming commonplace but often rely on closed-source and closed-format systems to access the data.
This was the case with the Olympus Virtual Slide Scanner microscope. We needed a way top open and process the large (>100k pixels) images in Fiji.
The result is an ActionBar that encompasses most common tasks required when opening and dealing with these large datasets: ROI management, On-demand (simplle) navigation and batch-processing.
The recommended method of installation is through http://imagej.net/Update_Sites:
- Install Fiji, not the Vanilla ImageJ
- Go to Help → Update
- Choose Manager Update Sites
- Check both the IBMP-CNRS and PTBIOP sites
- Restart Fiji
- You will find the BIOP VSI Reader under Plugins → BIOP → Importers → BIOP VSI Reader
All plugins and dependencies are automatically installed.
In case you would like to do the full installation yourself, please get in touch with us.
The source code can be accessed by opening the .ijm file containted in %FIJI%/plugins/BIOPBIOP_VSI_reader.jar (JAR files are basically zip files, so you can directly use 7zip, winzip or winrar to open it
We also have a repository here: https://c4science.ch/source/ijab-vsi-reader/
We've made a tutorial encompassing the most common steps here.