This pipeline is based on the study described in Li, Nuo, et al. "Amotor cortex circuit for motor planning and movement." Nature 519.7541 (2015): 51 with the data shared at http://crcns.org/data-sets/motor-cortex/alm-1/
All Jupyter notebooks in this catalog can be better viewed online through the Jupyter.org viewer at http://nbviewer.jupyter.org/github/datajoint-catalog
If you need a database account to try these examples, you can get a free tutorial account by subscribing through https://datajoint.io.
Before you start working with the pipeline, please obtain the following credentials:
- host address
- user name
The instructions for downloading the DataJoint library are available here: http://docs.datajoint.io/setup/Install-and-connect.html
Additionally, the common 'djcat-lab' module for general experiment data needs to be cloned from:
since it is referenced from this project. Be sure to setup your PYTHONPATH variable accordingly so that djcat-lab is included in sys.path. For example, your djcat-lab source code is stored in the same folder as this experiment, you can add it from within python as follows:
>>> import sys >>> import os >>> sys.path.insert(0, os.path.join('..','djcat-lab'))
Please submit issues and questions through the Issues tab above
The pipeline design
The [ALM1-erd.ipynb] notebook plots the entity-relationships diagrams (ERDs) for the ALM1.
It comprises two schemas:
lab for common elements across various studies and
alm1 for data specific to the ALM-1 study.
The entire pipeline
Source Data for ingest
Source data for this pipeline are available via CRCNS.org: http://crcns.org/data-sets/motor-cortex/alm-1
Data downloads require an account registration; Details are provided here: http://crcns.org/download
The example import scripts use the NWBv1 format files available within the datafiles/nwb_files subdirectory of the download area, and require the h5py library to be read.
More information concerning the NWB file format is available here: https://github.com/NeurodataWithoutBorders/specification
With the h5py library available via pip (pip install h5py). More details concerning h5py are available here: http://www.h5py.org/
The example export scripts are written using the NWB v1 API, available from: https://github.com/NeurodataWithoutBorders/api-python