Transition of the presynaptic vesicle cluster from a compact to dispersed organization during long-term potentiation

DOI:pnas.2522754123

Welcome to the repository for the manuscript titled "Transition of the presynaptic vesicle cluster from a compact to dispersed organization during long-term potentiation". This repository contains all the code created for this publication, for the analysis of the 3D reconstructions, biophysical simulations, and figures in the paper. Additional materials, such as electron microscopy images, 2D traces, and 3D reconstructions in Blender, are available here.

The /data/ folder contains a table of all measurements taken from the 3D reconstructions. In the /scripts_blender/ folder, you will find all the scripts created for analyzing the meshes. You can find the code used to generate the figures in the /scripts_figures/ folder. Additional analysis can be found in the /scripts_analysis/ folder. Finally, the code required to run the biophysical simulations is located in the /mcell_simulations/ folder.

All the scripts are written in Python version 3.9.19. The Blender version 2.79. was used to generate and analyze the 3D reconstructions. The following Python libraries were used for further analysis: Scipy version 1.11.4, Numpy version 1.21.6., Pandas version 1.4.0, Matplotlib version 3.8.2, Seaborn version 0.11.2, and Sklearn version 1.3.2. The computational model was run using MCell4.

Acknowledging the use of this material

Please cite the following paper:

Garcia G.C., Bartol T.M., Kirk L.M., Badala P., Harris K.M., and Sejnowski T.J. (2026) Transition of the presynaptic vesicle cluster from a compact to dispersed organization during long-term potentiation. PNAS 123 (22) e25227541.