nwb_datajoint

Setup

Instructions as of 09-02-2020

1. Clone this repository

   git clone https://github.com/LorenFrankLab/nwb_datajoint.git

2. Set up and activate the conda environment:

   cd nwb_datajoint
   conda env create -f environment.yml
   cd ..
   conda activate nwb_datajoint

3. Install the repo:

   cd nwb_datajoint
   python setup.py develop
   cd ..

   • Ignore the error error: numba 0.50.1 is installed but numba<0.49,>=0.37.0 is required by {'datashader'}

4. Use the datajoint docker installation

5. Temporary development package:

   ndx-franklab-novela (conda version too restrictive)

    git clone https://github.com/NovelaNeuro/ndx-franklab-novela.git
   
    cd ndx-franklab-novela
   

   open requirements.txt in your favorite text editor and remove the line hdmf==1.6.4

    vim requirements.txt
   

   install the repo

    python setup.py develop
   
    cd ..
   

6. Run populate_from_NWB_tutorial.ipynb from the notebooks directory.

7. Other examples: nwbdj_lfp_tutorial.ipynwb to extract LFP nwbdj_spikeinterface.pynwb to setup and run spikesorting