Channelpedia API

• Version 1.6: added matlab functions to retrieve and plot stimulus traces
• Version 1.5: whole review of python api
• Version 1.4: fixed axis labels; added get_stimulus in python/api.py
• Version 1.3: fix for compatibility with Python 3.7 (before only 3.6 was working)
• Version 1.2: bug fixes in matlab functions
• Version 1.1: added plot_features function for matlab

• Download and unzip the Channelpedia API.
• Place raw data downloaded from Channelpedia (e.g. rCell29308.nwb) in the Cells/ directory, and any downloaded analysis files (e.g. aCell29308.mat) in the Analysis/ directory.
• You can find the Python API scripts in the python/ directory, and the Matlab API scripts in the matlab/ directory.

Pre-requisites

• You need to have a valid Matlab installation. Please refer to the Mathworks support page for help.

Usage

• Start Matlab.
• In Matlab, make sure you're in the directory where the Channelpedia Matlab API script files are (matlab/). You can do so using the cd command, for example:

  >> cd 'C:\Users\Me\Download\channelpedia-api\matlab\'

• You can now use the provided functions to easily access or plot trace data. Available APIs are described in README.rst

Pre-requisites

• Python 3.5.x (or later) is required. If you have Python 2 installed (check running python -V in a terminal) your operative system likely needs it, and you should not upgrade it: it is recommended instead to install Anaconda with Python 3, https://www.anaconda.com/distribution/, through which you can open a special terminal with Python 3, when needed.

• The Channelpedia Python API requires a few Python modules to be installed; the easiest way to install them is using pip. If you've installed Python from the official website, you probably already have pip installed. To verify, run pip -V in a terminal. If not, to install pip run the following commands in a terminal:

  $ curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
  $ python get-pip.py --user

  Note: on certain Linux distributions, the pip version found in the distro's repositories may be outdated. In case of any errors when installing dependencies, it is recommended to install pip from the official source as shown above.
• Once pip is installed, you can have it fetch and install the required dependencies for the Channelpedia Python API.
  • Open a terminal inside the python/ directory.
  • Run the following command to have pip fetch and install the required dependencies:

    $ pip install -r requirements.txt --user

    Note: on some systems (e.g. Ubuntu), you may need to use pip3 instead of pip, as the latter may default to the Python 2.x version.
• (Optional) If you want to analyze raw data cells yourself, you'll also need to install the scipy Python module. For Linux/macOS users, simply run pip install scipy --user in a terminal to do so.
  For Windows users, download and install the following pre-built packages:
  • Note: download the appropriate package versions depending on the Python version you have installed ("cp35" if you have Python 3.5, "cp36" if you have Python 3.6) and architecture ("win32" for 32-bit Python, "win_amd64" for 64-bit Python).
    To find out your Python version, run the following command in a terminal:

    $ python -V

    To verify the architecture version, run the following command in a terminal:

    $ python -c "import platform; print(platform.architecture())"

  • Numpy+MKL: download the appropriate package then install it using pip. You can do so by opening a terminal in the directory where you downloaded the .whl file, then running the following command (modify the file name to point to the version you downloaded):

    $ pip install "numpy‑1.13.1+mkl‑cp35‑cp35m‑win32.whl" --user

  • SciPy: download the appropriate package then install it using pip as above, for example:

    $ pip install "scipy‑0.19.1‑cp35‑cp35m‑win32.whl" --user

Usage

• Open a terminal in the python/ directory and start the Python interpreter:

  $ python

• Import the Channelpedia Python API:

  >>> import channelpedia_api as api

• You can now use all the functions the API provides.
  Print the api documentation from the Python interpreter:

  >>> import channelpedia_api as api
  >>> help(api)