InsightSoftwareConsortium / InsightSoftwareConsortium/ITKElastix

Problem when opening a big TIF file

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Dominant language
Python
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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

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