bioimaging and optics platform BIOP

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VSI Reader ActionBar

O.Burri, R. Guiet

This ActionBar provides simple access to our Olympus Slide Scanner .VSI Files. Includes tools for extracting and resizing whole tissue scans.

Description

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 generated by the software 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 navigation and batch-processing.

Note:
You will need Jerome Mutterer's excellent ActionBar Plugin Installed if you're going to use the VSI Reader.

VSI Reader Image

Main VSI Reader Interface


Downloads

Download Documentation (PDF) Get Sample Dataset (250Mb)

Dataset kindly provided by  the Unité de Thérapie Cellulaire, headed by Prof. Laurent-Lee Applegate

Installation

The recommended method of installation is through Fiji Update Sites:

  1. Install Fiji, not the Vanilla ImageJ
  2. Go to 'Help' > 'Update'
  3. Choose "Manager Update Sites"
  4. Check both the 'IMBP-CNRS' and 'PTBIOP' sites
  5. Restart Fiji

All plugins and dependencies are automatically installed.

Dependencies: 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.


Figures

Another Figure

Fig. 1: "Load Selection": Sample dataset with a loaded selection.

Another Figure

Fig. 2: "Process ROIs": When processing multiple selections, you can rescale each image and run a predefined macro after each extraction.

References

No References as of yet



Contact

BioImaging and Optics platform (PTBIOP)

EPFL-SV-PTECH-BIOP
Station 15
CH-1015 Lausanne
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Dr. Arne Seitz

Office AI-0240
Tel: +41 (0) 21 693 96 18
Fax: +41 (0) 21 693 95 85