Ecephys and behavior workflows for the Mindscope Neuropixels team.
Project description
np_workflows
This package contains all the Python code required to run Mindscope Neuropixels experiments.
Experiment workflows and related tasks are coordinated by Jupyter notebooks maintained here: https://github.com/AllenInstitute/np_notebooks
Running the notebooks requires a Python environment with:
- Python >= 3.11
- np_workflows
- Jupyter / JupyterLab
git clone https://github.com/AllenInstitute/np_notebooks
conda create -n workflows python=3.11
pip install np_workflows
pip install jupyterlab
Keep the np_workflows
package up-to-date by running pip install np_workflows -U
before each use
To develop this package git clone
then pdm install
NP. rig setup
.venv is currently used, with PDM to update packages before each experiment:
- install JupyterLab desktop (Win 64-bit)
- clone
np_notebooks
(notnp_workflows
)cd c:\Users\svc_neuropix\Documents\github & git clone https://github.com/AllenInstitute/np_notebooks
- find the path to python.exe 3.11.*, or install it manually
- create a new venv in the
np_notebooks
dir:cd np_notebooks & path-to-python.exe -m venv .venv
- activate venv:
.venv\scripts\activate
(terminal should now report(np_notebooks-3.11)
) - install PDM in venv:
path-to-python.exe -m pip install pdm
- install
np_notebooks
requirements:pdm install
- in JupyterLab, set the default to Python environment to use
c:\Users\svc_neuropix\Documents\github\np_notebooks\.venv\scripts\python.exe
- open up any workflow in the
np_notebooks
dir and check that the initial cell with imports works
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