InsightSoftwareConsortium / InsightSoftwareConsortium/ITKElastix
Problem when opening a big TIF file
- Dominant language
- Python
- Stars
- 281
- Forks
- 29
- Avg merge
- 16h 28m
- Merged PRs (30d)
- 8
Description
Hello,
I am doing mouse brains alignement to the Allen Brain Atlas. Samples are optically cleared and images are obtained on a light sheet microscope.
It works nicely on small files (25x25x25 um voxel : 100 Mo in size).
However, when I am trying to apply the transformation to a high resolution data set of 70 Go, I have a problem: I cannot open the file at all:
- when using the view module from ITKWIDGETS, the big image looks empty.
- when trying to change the voxel spacing, it works on small size file but not on the big one.
If I crop the big one, it is opened correctly... That makes me think that the data type is good, but that it is some sort of memory problem.
I am working on Windows 10, with 512 Go Ram.
Thank you very much for your help!!
Best,
Jérémie
Contributor guide
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Research direction
Start by reproducing the report with the 70 GB TIF and a cropped version in the ITKWIDGETS view module, then compare the behavior when changing voxel spacing. Done means the full-resolution image opens correctly and voxel-spacing changes work without the empty display or failure reported for the large file.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- computer-vision
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100