Re: Memory issues with gigapixel files

Posted by Rutger Wierda on Jan 25, 2011; 3:22pm
URL: http://imagej.273.s1.nabble.com/Memory-issues-with-gigapixel-files-tp3685899p3685902.html

Dear Peter,

I'm not really sure whether I understand correctly what extra info you want to know from me, but I'll give it a try:

My TIFFs are originally exported from the microscopy software a 'tiled tiffs'. However ImageJ can't cope with tiled tiff files, so I open them in Photoshop CS5 and save them as regular 8-bit tiff files, with LZW compression. (interleaved pixel order, IMB PC byte order). The resulting files are opened in ImageJ (using file>open). So far this doesn't cause any problems. Then when I run the Color deconvolution plugin (I've downloaded it from the ImageJ website) the problem's start. When I run the nucleus counter plugin it seems that even more memory is needed. (In the nucleus counter, also downloaded from ImageJ's plugin section, I select Otsu 3x3 as thresold method and tick the watershed filter)

Maybe I could run the analysis on the separate tiles of the tiled tiff, however I have no clue whatsoever how to get the tiles out of the Tiffs and run them trough image J.

I hope this gives you the information you need,
Kind regards,

Rutger