Tools for uploading and interacting with Mindscope Neuropixels experiments on Code Ocean
Project description
np_codeocean
Tools for uploading and interacting with Mindscope Neuropixels experiments on Code Ocean
Requires running as admin on Windows in order to create remote-to-remote symlinks on the Isilon.
-
upload
CLI tool is provided, which uses thenp_session
interface to find and upload raw data for one ecephys session:pip install np_codeocean upload <session-id>
where session-id is a valid input to
np_session.Session()
:- a lims ID (
1333741475
) - a workgroups foldername (
DRPilot_366122_20230101
) - a path to a session folder (
\\allen\programs\mindscope\workgroups\np-exp\1333741475_719667_20240227
)
- a lims ID (
-
a folder of symlinks pointing to the raw data is created, with a new structure suitable for the KS2.5 sorting pipeline on Code Ocean
-
the symlink folder, plus metadata, are entered into a csv file, which is submitted to
http://aind-data-transfer-service
, which in turn runs theaind-data-transfer
tool on the HPC, which follows the symlinks to the original data, median-subtracts/scales/compresses ephys data, then uploads with the AWS CLI tool -
all compression/zipping acts on copies in temporary folders: the original raw data is not altered in anyway
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