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BIOP VSI Reader
Updated 2,069 Days AgoPublic
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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 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 ActionBar Plugin Installed if you're going to use the VSI Reader. See installation instructions below

Installation

The recommended method of installation is through http://imagej.net/Update_Sites:

  1. Install Fiji, not the Vanilla ImageJ
  2. Go to Help → Update
  3. Choose Manager Update Sites
  4. Check both the IBMP-CNRS and PTBIOP sites
  5. Restart Fiji
  6. You will find the BIOP VSI Reader under Plugins → BIOP → Importers → BIOP VSI Reader

All plugins and dependencies are automatically installed.

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.

VSIreader_tutov2.pdf1 MBDownload

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Last Author
oburri
Last Edited
May 2 2019, 10:30

Event Timeline

romainGuiet created this document.Sep 12 2018, 10:33
romainGuiet edited the content of this document. (Show Details)
romainGuiet changed the title from Ijab-biop Vsireader to ijab-BIOP VSI Reader.
romainGuiet edited the content of this document. (Show Details)
romainGuiet edited the content of this document. (Show Details)Sep 12 2018, 13:20
oburri changed the title from ijab-BIOP VSI Reader to BIOP VSI Reader.May 2 2019, 10:21
oburri edited the content of this document. (Show Details)
oburri edited the content of this document. (Show Details)
oburri edited the content of this document. (Show Details)
oburri edited the content of this document. (Show Details)May 2 2019, 10:30
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