Tutorials

kcsd-python library comes with three extensive tutorials. These tutorials can be explored online or installed on your desktop computer depending on your usage. To simple test it out try the online version first, and if required install the python package.

Online version

To play around with the library without any installation, you can run the tutorials on Google collaboratory in a web-browser. Note: the results from a browser are not saved and cannot be retreived. If you wish to have the results stored somewhere, please use the desktop version.

Desktop version

This requires you to install the kCSD-package and additionally to install jupyter notebook on your desktop.

pip install kcsd
pip install jupyter notebook

Basic Features

This tutorial showcases, the use of the kCSD-python package in the case of the simplest 2D square grid of electrodes. It defines a region where can place true current sources, probe it with a grid or electrodes, based on these measurements and using the proposed method, estimate the CSD. Since we also know the true sources, we can now estimate the error in the estimation method as well. To this preliminary setup, we add noise to the measurements at the electrodes, and repeat the procedure. We also explore the situation when certain number of the electrode are broken, and how that would effect the reconstructions.

The tutorial is provided with Google collaboratory, click the button below to interact with it in a browser, no installation necessary.

Basic tutorial

For a non-interactive static version of this tutorial, see Tutorial1.

Advanced Features

This tutorial showcases many more features of the kcsd-python package, especially the cases when the electrodes are distributed in 1D (laminar probe like), 2D (Neuropixel like), 3D (Utah array like) or on a microelectrode arrays (MEA, slice with saline). It is provided with buttons and easy clickable interface to enable the user to navigate the otherwise dense details. In some ways, it extends on the Basic Features tutorial and expands it to the other dimensions. NOTE, the user might have to ‘Reset this tutorial’ before using to enable the buttons (Kernel>Restart & Run All).

The tutorial is provided with Google collaboratory, click the button below to interact with it in a browser, no installation necessary.

Advanced tutorial

For a non-interactive static version of this tutorial, see Tutorial2.

sKCSD Tutorial

This tutorial showcases the possibility to reconstruct the current sources of a single neuron provided the morphology of the said neuron is known. This methods has been described extensively here: https://doi.org/10.7554/eLife.29384

sKCSD tutorial

For a non-interactive static version of this tutorial, see sKCSD Tutorial

More Tutorials

There are many more ways to test this method some of these can be made into tutorials for easier understanding. While we are working on this, they will appear here once they reach production level. Please watch-out this space in the near future. We also take requests for tutorials.

Do you wish there was a tutorial for your setup? Can you provide us with the electrode positions and some sample recordings under open license? If so, we might be able to tailor-make a tutorial for you! Please get in touch. See Contacts.