Coupling of MINI2P with corrected microendoscopes - code

This is the companion repository to the manuscript:
Extended field-of-view two-photon imaging in the deep brain of freely behaving mice using lightweight microfabricated corrective optics
It contains the following 3 folders.

Optical_characterization

This folder contains 3 Python notebooks for the analyses of optical characterization measurements performed with the MINI2P alone, the MINI2P coupled with the 4.1 mm-long microendoscope and the MINI2P coupled with the 6.4 mm-long microendoscope, plus a Fiji macro used to generate and evaluate the size of lateral and axial projections of fluorescent beads.

Trace_extraction

This folder contains the Python notebook used to extract single-cell fluorescence traces from in vivo MINI2P recordings using CITE-On (Sità et al., Nat. Commun. 2022).

HD_tuning

This folder contains 4 Python notebooks for the analyses of head-direction tuning in thalamic neural populations during open field navigation. The notebooks contain the code for: identification of head-direction cells, fitting head-direction tuning curves with von Mises models, analysis of the spatial distribution of head-direction cells, and generation of figures reported in the manuscript.

Contributing authors

Chiara Nardin1,*, Andrea Sattin1,*, Sebastiano Curreli1,*, Giorgio Letti1,2, Laura Maddalena1, Leonardo Nacci1, Tommaso Fellin1,#
1 Optical Approaches to Brain Function Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
2 University of Genova, Genova, Italy
* Equal contribution
# Corresponding author: tommaso.fellin@iit.it