Skip to content

Tools for accessing data, metadata, and jobs related to ecephys and behavior sessions for the Mindscope Neuropixels team.

Notifications You must be signed in to change notification settings

AllenInstitute/np_session

Repository files navigation

np_session

For use on internal Allen Institute network

A lightweight package for handling file paths and metadata associated with Mindscope Neuropixels experiments with data on local rig-connected machines or the /allen network. Provides an interface that can be used by other applications.

>>> from np_session import Session

# initialize with a lims session ID or a string containing one: 
>>> session = Session('c:/1116941914_surface-image1-left.png') 
>>> session.lims.id
1116941914
>>> session.folder
'1116941914_576323_20210721'
>>> session.is_ecephys
True
>>> session.rig.acq # hostnames reflect the computers used during the session, not necessarily the current machines
'W10DT05515'

# some properties are objects with richer information:
>>> session.mouse
Mouse(576323)
>>> session.project
Project('NeuropixelVisualBehavior')

# - `pathlib` objects for filesystem paths:
>>> session.lims_path.as_posix()
'//allen/programs/braintv/production/visualbehavior/prod0/specimen_1098595957/ecephys_session_1116941914'
>>> session.data_dict['es_id']
'1116941914'

# - `datetime` objects for easy date manipulation:
>>> session.date
datetime.date(2021, 7, 21)

# - dictionaries from lims (loaded lazily):
>>> session.mouse.lims
LIMS2MouseInfo(576323)
>>> session.mouse.lims.id
1098595957
>>> session.mouse.lims['full_genotype']
'wt/wt'

# with useful string representations:
>>> str(session.mouse)
'576323'
>>> str(session.project)
'NeuropixelVisualBehavior'
>>> str(session.rig)        # from `np_config` package
'NP.0'

Adding a new project

  • Add an enum with any project identifiers (e.g. lims project code) to components.info.Projects

  • Create an entry for lims manifests (if applicable) in Zookeeper at projects/np_session/manifests

    • the D1 manifest will need customizing (see other entries)
    • the default D0 and D2 manifests will likely suffice: nothing needs to be done

About

Tools for accessing data, metadata, and jobs related to ecephys and behavior sessions for the Mindscope Neuropixels team.

Resources

Stars

Watchers

Forks

Languages