Re: BioFormats Issues

Posted by baselta on May 28, 2015; 1:30am
URL: http://imagej.273.s1.nabble.com/BioFormats-Issues-tp5012620p5012961.html

Hi Olivier...
I'm a new user to VSI Reader/Bio-Format and I'm facing the same issue.
I uninstalled the latest Fiji and reinstalled the November 2014 release. I then added ActionBar plugin. Then I went to Help>Update Fiji and added auto-update for BIOP, however before accepting changes I "keep as is" all the suggested updates except BIOP. I restarted the software, then went again to Update Fiji and updated Bio-Format. After all this hassle it finally worked. I however don't know if it worked properly or not since this is the first time I used this.

I also found this on Bio-Format website:
"If you get an OutOfMemory or NegativeArraySize error message when attempting to open an SVS or JPEG-2000 file then the amount of pixel data in a single image plane exceeds the amount of memory allocated to the JVM or 2 GB, respectively. For the former, you can increase the amount of memory allocated; in the latter case, you will need to open the image in sections. If you are using Bio-Formats as a library, this means using the openBytes(int, int, int, int, int) method in loci.formats.IFormatReader. If you are using Bio-Formats within ImageJ, you can use the Crop on import option.

Note that JPEG-2000 is a very efficient compression algorithm - thus the size of the file on disk will be substantially smaller than the amount of memory required to store the uncompressed pixel data. It is not uncommon for a JPEG-2000 or SVS file to occupy less than 200 MB on disk, and yet have over 2 GB of uncompressed pixel data."


Thanks.
Basel