Diffusion VSI Reader ActionBar (master)

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VSI Reader ActionBar
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DESCRIPTION: Simple Action Bar to open and make sense of the Olympus OlyVIA Slide Scanner
The macro works as follows
Uses Jerome Mutterer's Action Bar Plugin as the interface.
Takes advantage of the print "Update" Function as of IJ 1.38m to keep data in memory.
Uses LOCI BioFormats to read and parse the data from the VSI reader

MOTIVATION: Images produced by the OlyVIA Scanner are extremely large (>48'000px)
The inherent limitation of Java (or IJ) for images is about 48'000px Because the .vsi files have preview thumbnails, we want to use those in order to navigate the data and open only the part of the image we're interested in.

VSI Reader ActionBar (master)

BIOP_VSI_reader.ijm
BIOP_VSI_reader.jar
Readme.md
icons/
plugins.config
updateJar.bat

Recent Commits

Commit	Author	Details	Committed
a8a781a0c5bd	oburri	fixes format issues and adds sanity check if roiset is present but not VSI file	Dec 21 2018
47939348bf10	oburri	adds internal setting to fix VSO Bioformats C<->Z bug	Sep 4 2018
b87564e7290d	oburri	Merge branch 'master' of https://c4science.ch/diffusion/944/ijab-vsi-reader	Mar 8 2018
908b6618ec40	oburri	New location	Mar 8 2018
39e90959e414	oburri	Adds documentation explaining recent fixes fixes a bug where ROI export no…	Feb 1 2018
9f84d83f574a	oburri	Adds documentation explaining recent fixes	Jan 29 2018
cf3418dc3840	oburri	Fixes thumbnail images being left open after the Extract All Command	Jan 29 2018
2219b7031c48	oburri	changes menu entry name from VSI Reader to BIOP VSI Reader	Jan 29 2018
e2d5e269a7aa	oburri	fixes location of ijm file during debugging	Jan 29 2018
56da0d5333ee	oburri	adds better support for VSI files with different imaging modalities	Jan 29 2018
8d7e1fd47a5f	oburri	does not preselect all series if more than 4	May 2 2017
06b09ddeb521	oburri	adds Readme.md	Oct 7 2016
00c31f43a3d4	oburri	Fixes ROI Deletion issues as well as indexing of ROIs when batch opening files…	Oct 7 2016
b61ef58d1ee0	oburri	adds debug timing measurements and fixed a bug where the current roi was not…	May 31 2016
51eca762bada	oburri	Merge branch 'master' of https://git.epfl.ch/repo/biop-vsi-reader	Feb 3 2016

Readme.md

BIOP VSI READER

Installation as an End User

Simply activate the PTBIOP and IBMP-CNRS Update Sites in Fiji. It will be under

Plugins > BIOP > BIOP VSI Reader

Installation in order to make modifications

To edit this ActionBar, place the BIOP_VSI_Reader.ijm file in your Plugins/ActionBar folder.

Then you can open it in Fiji. To work in debug mode, uncomment line 36

runFrom = "jar:file:BIOP/BIOP_VSI_reader.jar!/BIOP_VSI_reader.ijm";

33. //////////////////////////////////////////////////////////////////////////////////////////////
34. // The line below is for debugging. Place this VSI file in the ActionBar folder within Plugins
35. //////////////////////////////////////////////////////////////////////////////////////////////
36. //runFrom = "/plugins/ActionBar/BIOP_VSI_reader.ijm";

When you are finished, you must re-comment the above line, and repackage the file as a JAR. You can have a look at the updataJar.bat file in this repository. Alternatively, opening the JAR using winRAR or 7-ZIP and placing the modified IJM file inside works just fine.