Update data export scripts #54
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
constantinpape
commented
Jul 25, 2025
scripts/export_lower_resolution.py
Outdated
| segmentation[filter_mask] = 0 | ||
|
|
||
| # segmentation, _, _ = relabel_sequential(segmentation) | ||
| segmentation, _, _ = relabel_sequential(segmentation) |
Contributor
Author
There was a problem hiding this comment.
I think that this is the culprit why IHC ids and synapse IDs don't match. We still need to be careful here though, if the max ID exceeds 65,... than we run out of uint16 IDs, which may happen for SGNs and is why I included this.
Maybe the best option is to remove the sequential relabeling here, and to raise a warning if we have larger values than the uint16 max id, as this won't lead to a big issue, just some ID clashes.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.