Tools and interfaces for working with behavior and epyhys sessions from the Mindscope Neuropixels team, in the cloud.
Project description
npc_sessions
neuropixels cloud sessions
Tools for accessing data and metadata for behavior and epyhys sessions from the Mindscope Neuropixels team - in the cloud.
quickstart
Make a conda environment with python>=3.9 and simply pip install the npc_sessions package:
conda create -n npc_sessions python>=3.9
conda activate npc_sessions
pip install npc_sessions
>>> from npc_sessions import DynamicRoutingSession, get_sessions;
# each object is used to get metadata and paths for a session:
>>> sesssion = DynamicRoutingSession('668755_2023-08-31')
>>> session.is_ephys
True
>>> session.stim_paths[0].stem
'DynamicRouting1_626791_20220815_112336'
# data is processed on-demand to generate individual pynwb modules:
>>> session.subject
subject pynwb.file.Subject at 0x...
Fields:
age: P145D
age__reference: birth
date_of_birth: 2022-03-22 20:22:03-07:00
genotype: wt/wt
sex: M
species: Mus musculus
strain: C57BL6J(NP)
subject_id: 626791
# a full NWBFile instance can also be generated with all currently-available data:
>>> session.nwb # doctest: +SKIP
root pynwb.file.NWBFile at 0x...
Fields:
acquisition: {
lick spout <class 'ndx_events.events.Events'>
}
devices: {
18005102491 <class 'pynwb.device.Device'>,
18005114452 <class 'pynwb.device.Device'>,
18005123131 <class 'pynwb.device.Device'>,
18194810652 <class 'pynwb.device.Device'>,
19192719021 <class 'pynwb.device.Device'>,
19192719061 <class 'pynwb.device.Device'>
}
...
# loop over all currently-tracked ephys sessions using the session-generator:
>>> all(s.session_start_time.year >= 2022 for s in get_sessions())
True
>>> trials_dfs = {}
>>> for session in get_sessions(): # doctest: +SKIP
... trials_dfs[session.id] = session.trials[:]
to develop with conda
To install with the intention of contributing to this package:
- create a conda environment:
conda create -n npc_sessions python>=3.9
conda activate npc_sessions
- clone npc_sessions from github:
git clone git@github.com:AllenInstitute/npc_sessions.git
- pip install all dependencies:
cd npc_sessions
pip install -e .
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