kcsd-python library comes with two extensive tutorials (at this moment, more soon). These can be tested using Jupyter notebook on your desktop after installing the kCSD-python package. Alternatively, they can be played around with without any installation on Binder in a web-browser. Note that in this case, the results from a browser are not saved, and cannot be retreived.
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 Binder access, click the button below to interact with it in a browser, no installation necessary.
For a non-interactive version of this tutorial, see `Tutorail1<https://github.com/Neuroinflab/kCSD-python/blob/master/tutorials/tutorial_basic.ipynb>`_.
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 Binder access, click the button below to interact with it in a browser, no installation necessary.
For a non-inteactive version of this tutorial, see `Tutorail2<https://github.com/Neuroinflab/kCSD-python/blob/master/tutorials/tutorial_advanced.ipynb>`_.
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.