Re: Memory issues with gigapixel files

Posted by Peter Haub on Jan 26, 2011; 8:14am
URL: http://imagej.273.s1.nabble.com/Memory-issues-with-gigapixel-files-tp3685899p3685903.html

As Gabriel suggest
either cut your image into smaller once by copy ROI and paste into new
smaller images (you can not directly extract the TIFF internal tile
structure into separated images)
or resize your image,
or use a 64bit OS and more memory
or check if your microscopy software can save the image in several
images instead of one gigapixel image.

  Peter

Am 25.01.2011 16:22, schrieb Rutger Wierda:

> 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
>