AllenNeuralDynamics / AllenNeuralDynamics/aind-SmartSPIM-segmentation

Initialize Neuroglancer at t=0 to avoid odd behavior

Open
#21 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
4
Forks
1
Avg merge
4d 4h
Merged PRs (30d)
1

Description

Viewer links for the cell segmentation states behave differently than the stitched volume links. See [here](https://github.com/google/neuroglancer/issues/772).

This boils down to the initial position of the viewer being at t=0.5. When a user presses z to snap a rotation to the nearest data-aligned axes, the time axis snaps to t=1, which is out of bounds for the zarr volume and causes the image to disappear.

The nglink functions used to create the stitched volume link must take care of this, since the behavior is not observed there. I think the position can easily be added here:
https://github.com/AllenNeuralDynamics/aind-SmartSPIM-segmentation/blob/4d6b2495bbcf442c547dd73e0d227e88ff93a72e/code/aind_smartspim_segmentation/segmentation.py#L318

Contributor guide

No contributing guide indexed for this repository

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.