Re: bfconverter nd2 to tif

Posted by Greg on Mar 24, 2015; 3:35pm
URL: http://imagej.273.s1.nabble.com/bfconverter-nd2-to-tif-tp5012133p5012136.html

Hi Curtis,

ok thanks for the clarification about the tif formats. So my target format would definitely be the ImageJs 'raw' TIFF, as all operations seem to be much faster with that format. I still see no way of doing the conversion without loading the whole stack into memory. And with 'lagginess' I mean especially the performance after loading the file, so switching to next frame for example. So bascically I see no performance difference in between BigTIFF and the proprietary nd2 format, and it is also essentially the same if I open them as virtual stack or not.. so ya, I migth start a thread on the ome site you pointed me to.

The Hyperstack problem turned out to be a bit more serious, as again to make the output of the bfconverter a Hyperstack, I see no other way as loading the whole Stack into memory as the Hyperstack information is lost in BigTIFF format ?!

So instead of doing nice image analysis with jython in Fiji, I am now more or less lost in a jungle of formats and memory problems, I guess that is the fate of the life cell image analyst :P

Best,
Greg