Simulation of Ca2+ dynamics in astrocyte leaflets

Matlab class and helper functions to simulate astrocytic calcium and sodium dynamics in thin astrocytic processes of genuine, experimentally obtained geometries.

To simulate Ca2+ dynamics in experimentally determined synapses, do the followings:

1. Add the @Synapse folder to your path in Matlab

2. Download our pre-processed synapse data based on the Kasthuri et al., 2015. It contains 1700 selected synapses. http://downloadables.ttk.hu/heja/Front_Cell_Neurosci_2021/vastSynapses.mat

3. Load this file to Matlab: load("vastSynapses.mat");

4. Now, we will run a simulation on the first synapse in this database.

5. Since tissue is shrinked in the EM samples, we need to correct for the shrinkage: synapses(1).correctECS;

6. Clear previous simulation data: synapses(1).simulationClear;

7. Run the simulation: synapses(1).simulationRun;

8. The simulation results can be viewed at synapses(1).Simulation or you can export it to a .mat file: synapses(1).simulationExport("synapse1_simulation");

Citation

If you find this tool useful, please, cite the following publication: Heja L, Szabo Z, Peter M, Kardos J. Spontaneous Ca2+ Fluctuations Arise in Thin Astrocytic Processes With Real 3D Geometry. Front Cell Neurosci., 15:617989, 2021 https://doi.org/10.3389/fncel.2021.617989