Importing ROIs and transformations from QuPath
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- Dominant language
- Python
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- 394
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Description
To align an image to a reference atlas I used ABBA to apply some transformations via elastix and bigwarp. I then exported the registrations to QuPath where I can see the atlas segmentations on the original image. I also see that it generates a json file that describes the transformations that were applied to my image. (Example below) In theory I think I should should be able to use this to create an "atlas aligned" coordinate system in spatial data? And I could also import the ROIs as shapes?
"realTransform_2": {
"type": "AffineTransform3D",
"affinetransform3d": [
999.9999999999999,
0.0,
0.0,
405.0,
0.0,
999.9999999999999,
0.0,
421.99999999999994,
0.0,
0.0,
999.9999999999999,
0.49999999999999994
]
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Research direction
The issue names no repository files, tests, or entry points. Clarify whether the goal is importing QuPath ROIs, applying the JSON transformations, creating an atlas-aligned coordinate system, or all three before locating the relevant spatial-data entry points and defining completion criteria.
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Assessment
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100