Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Compatibility with SpikeGLX 20230202-phase30 or later #168

Closed
ttngu207 opened this issue Jul 20, 2023 · 0 comments · Fixed by #169
Closed

Compatibility with SpikeGLX 20230202-phase30 or later #168

ttngu207 opened this issue Jul 20, 2023 · 0 comments · Fixed by #169
Assignees
Labels
enhancement New feature or request

Comments

@ttngu207
Copy link
Contributor

Feature Request

Problem

This is originally reported by Scott Bolkan from the Princeton BRAINCoGS group.

the root source however i think is that SpikeGLX release 2023-02-02 onward has removed snsShankMap from the neuropixels/imec meta data (it's now replaced with snsGeomMap). i think some code in the datajoint ephys element looks for snsShankMap in order to create configuration files for spikesorting with kilosort. for example, my newly acquired neuropixels 2.0 data with the latest SpikeGLX fails in the follow princeton-u19 ephys pipeline:

File "/home/u19prod@pu.win.princeton.edu/miniconda3/envs/U19-pipeline_python_env/lib/python3.9/site-packages/element_array_ephys/ephys_precluster.py", line 187, in make
   for shank, shank_col, shank_row, _ in spikeglx_meta.shankmap['data']]
TypeError: 'NoneType' object is not subscriptable

Jennifer Colonell has shared code for adding snsGeomMap fields to ap.meta files acquired in older versions of SpikeGLX here

@ttngu207 ttngu207 added the enhancement New feature or request label Jul 20, 2023
@kabilar kabilar moved this to 🚀 Active in DataJoint Open-Source Software Jul 26, 2023
@ttngu207 ttngu207 moved this from 🚀 Active to 👀 In review in DataJoint Open-Source Software Jul 27, 2023
@ttngu207 ttngu207 moved this from 👀 In review to 🚀 Active in DataJoint Open-Source Software Jul 27, 2023
@github-project-automation github-project-automation bot moved this from 🚀 Active to ✅ Done in DataJoint Open-Source Software Sep 16, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
Status: Done
Development

Successfully merging a pull request may close this issue.

1 participant