Re: VSI Plugin for Fiji

[Olivier Burri]

Dear Prof. Singh,

We found the limit to be around 48Kx48K on our 64-bit systems. If you are running a 32-bit version it is possible you're hitting the memory limit before us and it would explain the 2GB limit of Java on your system.

A few things to try out is to go to Edit->Options->Memory and Threads
Then make sure that most of your RAM is allocated to Java.

Alternatively you can follow the steps outlined here. They apply to TrakEM2 but are very useful for any heavy-duty Fiji use as well.
http://fiji.sc/wiki/index.php/TrakEM2#Running_fiji_for_heavy-duty.2C_memory-intensive.2C_high-performance_TrakEM2_tasks

Note that if you are running on a 32-bit System, the 2GB limit still applies. I seem to recall you can get around it with some fiddling under WinXP but I'd recommend getting a 64-bit machine with >8GB RAM if you want to be comfortable with large datasets.

I'm adding this to the ImageJ / Fiji mailing list as it could be useful to others.

Best

Oli


Olivier Burri
Engineer - Image Processing
& Software Development
EPFL - SV - PTECH - PTBIOP

From: Singh, Jaswant [mailto:[hidden email]]
Sent: jeudi 10 avril 2014 15:02
To: Burri Olivier
Subject: Re: VSI Plugin for Fiji

Thank Oli.
Update site worked very well. My VSI images are more than 14Kx10K pixels and I am able to open these at 0.25 downsampling. Do you know the largest XY dimensions that Fiji will allow me to open. Is it still 2 gegapixels JAVA limit for current version of Fiji or do we have some other way-out. Thanks for your help in advance.
Jaswant Singh
_________________________________
Professor and Graduate Chair
Veterinary Biomedical Sciences
University of Saskatchewan
52 Campus Drive
Saskatoon SK S7N 5B4 Canada
306-966-7410
_________________________________




On Apr 10, 2014, at 1:32 AM, Burri Olivier <[hidden email]<mailto:[hidden email]>> wrote:


Dear Prof. Singh,

The easiest way is to activate our Update Site in Fiji
http://fiji.sc/List_of_update_sites

We are PTBIOP in that list. If you go to Help>Update Fiji>Manage Update Sites
You can tick our update site from the list.

Otherwise the ZIP file on our webpage is now available for download. A bug on my behalf was the cause for the 404 error.

All the best

Oli


Olivier Burri
Engineer - Image Processing
& Software Development
EPFL - SV - PTECH - PTBIOP

From: Singh, Jaswant [mailto:[hidden email]]
Sent: mardi 8 avril 2014 00:07
To: Burri Olivier
Subject: VSI Plugin for Fiji

Hi Oliver:
I am trying to install the Plugin for reading VSI files into Fiji and I have already installed the "Action Bars" plugin. Somehow the link given for download button in your "http://biop.epfl.ch/TOOL_VSI_Reader.html" page is not working. I must admit that I am a novice as far as Fiji/Image J plug-ins and macros are concerned. Could you please advice where to get the most recent version and how to install it.
Thank you
Jaswant Singh
_________________________________
Professor and Graduate Chair
Veterinary Biomedical Sciences
University of Saskatchewan
52 Campus Drive
Saskatoon SK S7N 5B4 Canada
306-966-7410
_________________________________


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