Re: MetroloJ plugin help

Posted by Jacqueline Ross on Apr 29, 2015; 6:36am
URL: http://imagej.273.s1.nabble.com/MetroloJ-plugin-help-tp5012622p5012643.html

Hi Matthew,

Yes, you do need a z stack to use this plugin. It's a fantastic tool for testing your microscope.

I used it when I was involved in a global ABRF study a few years ago. A Nature Protocols paper came out of that work
 - http://www.nature.com/nprot/journal/v6/n12/full/nprot.2011.407.html

There are instructions on the Fiji website here: http://imagejdocu.tudor.lu/lib/exe/fetch.php?media=plugin:analysis:metroloj:matthews_cordelieres_-_imagej_user_developer_conference_-_2010.pdf

I also have another instruction file as PDF that I can send you offline if you want it. Just email me directly for that.

Cheers,

Jacqui

Jacqueline Ross
Biomedical Imaging Microscopist
Biomedical Imaging Research Unit 
School of Medical Sciences 
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland 1142, NEW ZEALAND

Tel: [phone]
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of PEARSON Matthew
Sent: Monday, 27 April 2015 10:25 p.m.
To: [hidden email]
Subject: MetroloJ plugin help

Hi all,

I'm not sure if this is the best mailing list for this issue but i have tried to contact the developers but their email addresses are no longer active.

I have been using the metroloJ plugin:
http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:metroloj:start

I have captured 3 images each an image a plastic fluorescent slide (blue, green & red) in order to run them through the Coefficient of Variance (CV) feature of the plugin.  However, when i run the plugin on one of these images it allows me to draw a ROI on the image and i select to save the files but then i get a JAVA error:

(Fiji Is Just) ImageJ 2.0.0-rc-29/1.49r; Java 1.6.0_65 [64-bit]; Mac OS X 10.6.8; 71MB of 1943MB (3%)

java.lang.ArrayIndexOutOfBoundsException: 4043 at metroloJ.cv.cv.getHistograms(cv.java:268)
at metroloJ.report.CVReport.saveReport(CVReport.java:115)
at Generate_CVreport.run(Generate_CVreport.java:62)
at ij.IJ.runUserPlugIn(IJ.java:199)
at ij.IJ.runPlugIn(IJ.java:163)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:695)

I wasn't sure if i had to acquire a z stack and perhaps the fact i only have a single image is the issue?

Thanks for any help,

Matt




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