Comments (2)
SaibotMagd
commented on July 26, 2024
Update: it seems like the autofluorescence picture got a very bright border. Could this lead to the wrong calculation of translation parameters (last 3 parameters in the affine parameter array)? Probably, so how to solve it?
It seems like quality of the autofluorescence data just isn't good enough. I couldn't find out how to validate what "good" is. Hopefully the upcoming samples will clear this out.
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ywang219
commented on July 26, 2024
Hello,
Thank you for sharing your troubleshooting steps here. Could you elaborate if you got a better alignment for the new samples?
I have run into issues on alignment quality too, some brains have bright spots on the borders, and some have a little distorted brain regions. Do you think it could be how the brains were orientated in the light-sheet? We tried to have them run under the same conditions, same orientations...
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Related Issues (20)
- Cell alignment section - file not found error HOT 1
- Cannot find name for type 'elastix_resampled_to_auto'! HOT 1
- How to generate intensity profile? HOT 2
- Alignment of warped atlas to autofluorescence looks correct but overlay of raw atlas with transformed cells appears wrong. HOT 1
- TubeMap: "IndexError: list index out of range" while runnin the cell of Rigid z-alignment HOT 1
- Stitching parameters for persistent duplications
- TubeMap Create a test data
- Spyder 5.2.2 incompatible to Anaconda 3 HOT 1
- TypeError: key must be an int, slice, or sequence HOT 5
- Bug: inverse transform HOT 1
- registration troubleshooting
- Cell Annotation Didn't Work... HOT 2
- clearmap results ID different than Allen Region ID HOT 1
- Annotated_counts table counts area and their subdivision differently HOT 1
- Adding CCFv3 annotation requires updating the "No label" values
- Problem Plotting 3d Mesh HOT 2
- Resampling IndexError: tuple index out of range HOT 4
- Question about the unit of vasculature radius HOT 1
- Duplicate maxima coordinates detected with different 'source' and 'size' measurements
- Elastiz error HOT 1
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