Lineage Connectomics

Watch our NeuroMatch 4.0 Talk!

Data

Connectomes

witvliet2021-Dataset8.graphml

This dataset is downloaded at runtime from MossDB. A copy is cached in data/.

Lineages

bhatla-lineage.json

This dataset was generated by evaluating the JavaScript object provided here and copying to JSON. This can be most easily done by pasting the data into a browser JS console:

copy(JSON.stringify(...));

Or by calling the getJson() function on this page:

copy(JSON.stringify(getJson()));

Cell Locations

We need a way to determine a cell location for each cell so that we can talk meaningfully about cell "distances" in Euclidean space. Unfortunately, the easiest way I can think of to do this is to go to the OpenWorm .blend Blender 3D model and capture the origins of all neuron cell meshes.

The script to accomplish this is stored in preprocessing/get-blender-centroids.py. Note that this Python code will NOT run in "plain" Python; it MUST be run from inside Blender.

You can download the source material from this website.

We use the latest Feb 2012 version.

Usage

To create the figures in figs/, the Analysis.ipynb notebook is run twice; first with the NULL_MODEL parameter set to True, and then with the NULL_MODEL parameter set to False. This creates fig-grouped-distance-null.svg and fig-grouped-distance.svg in figs/