This code is associated with the paper from Antonini et al., "Extended field-of-view ultrathin microendoscopes for high-resolution twophoton imaging with minimal invasiveness". eLife, 2020. http://doi.org/10.7554/eLife.58882
Simulations code for Antonini et al, 2020, bioRxiv
This code generates artificial time series from synthetic data. It randomly places somas in a given volumes and simulates their spiking activity. Then, simulates the imaging of the artificial volume with two different types of endoscopes, one without correction for aberrations and one with aberration correction.
The accompanying paper is:
Extended field-of-view ultrathin microendoscopes for high-resolution two-photon imaging with minimal invasiveness in awake mice
Andrea Antonini, Andrea Sattin, Monica Moroni, Serena Bovetti, Claudio Moretti, Francesca Succol, Angelo Forli, Dania Vecchia, Vijayakumar P. Rajamanickam, Andrea Bertoncini, Stefano Panzeri, Carlo Liberale, Tommaso Fellin
2020, bioRxiv, doi: https://doi.org/10.1101/2020.05.14.095299
Before running the code for simulations, some auxiliary files must be downloaded from DOI: 10.17632/wm6c5wzs4c.1 (dataset_3, folders imaging_ellipsoids, intensity_mask, psf_estimate, ruler_FOV) and added to the main folder.
Parameters for the simulations are set in main_simulate_TSeries_only.m
Details:
- required software: Matlab R2019b