[ome-users] ndpi-files: stack processing

[MEYENHOFER Felix]

Hi 

along the lines of the question that I raised in the thread:
"java.lang.illegalArgumentException: Array size too large” (18. March 2015)

We are currently trying to process stacks that are saved in the ndpi format. In the example I put on the dropbox
https://dl.dropboxusercontent.com/u/18607042/test5_stack_ROI01.ndpi

if I open series 1 (Hyperstaack xycz, split channels, virtual stack), it is executed without error. However, it seems, that only one frame is opened, going through the stack all frames seem identical. This obviously is not the case.
So Melissa pointed out to me that images can not have more than 2GB of pixels. But in this case a frame (of series 1) has ~4.5M pixels. The entire stack is ~2.1GB. Since there is no error in the imagej console, I assume the 2GB limit applies per frame. But I was unable to figure out why the frames in the stack look all the same…

I could use some information about how the stacks are handled in the current Bio-Formats.

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Felix Meyenhofer
University of Fribourg
Departement of Medicine - Anatomy
1, Rte. Albert Gockel
CH-1700 Fribourg 

Tel:  +41 26 300 85 45
Web:  www.unifr.ch/anatomy
      www.unifr.ch/bioimage
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