Whole brain cell detection and registration with the cellfinder command line tool#

Although the cellfinder command line tool is designed to be easy to install and use, if you’re coming to it with fresh eyes, it’s not always clear where to start. We provide an example brain to get you started, and also to illustrate how to play with the parameters to better suit your data.


The test dataset is large (~250GB). It is recommended that you try this tutorial out on the fastest machine you have, with the fastest hard drive possible (ideally SSD) and an NVIDIA GPU.


The tutorial is quite long, and is split into a number of sections. Please be aware that downloading the data, and running cellfinder may take a long time (e.g., overnight x2) if you don’t have access to a particularly high-powered computer, or fast network connection.

Please go through the following sections in order: