WARNING: This tool was developed between 2014 and 2016 for our needs with the time and resources we had available. We are happy that so many people find it useful and are happy to provide limited support.
However, within our facility, **we have phased out use of the VSI reader in favor of [[https://qupath.github.io/|QuPath]]**, which can directly handle VSI files using Bioformats, and removes data duplicating steps.
= Authorship =
**Olivier Burri, Romain Guiet, Arne Seitz**
//BioImaging & Optics Platform (BIOP)//
**Ecole Polytechnique Fédérale de Lausanne**
= Description =
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.
NOTE: You will need Jerome Mutterer's excellent [[http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:action_bar:start|ActionBar Plugin]] Installed if you're going to use the VSI Reader. **See installation instructions below**
=Installation=
The recommended method of installation is through [[Fiji Update Sites|http://imagej.net/Update_Sites]]:
# Install [[https://fiji.sc|Fiji]], not the Vanilla ImageJ
# Go to {nav Help > Update}
# Choose {nav Manager Update Sites}
# Check both the **IBMP-CNRS** and **PTBIOP** sites
# Restart Fiji
# You will find the **BIOP VSI Reader** under {nav Plugins > BIOP > Importers > BIOP VSI Reader}
All plugins and dependencies are automatically installed.
(NOTE) **Exhaustive Dependency List:** BIOP Macro Library Installer and BIOP Macro Library (Internal) and ActionBar.
In case you would like to do the full installation yourself, please get in touch with us.
=Source Code=
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/
=Tutorial=
We've made a tutorial encompassing the most common steps here.
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=Display=
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