Synthetic calcium data for the 6.4 mm-long uncorrected microendoscope

This dataset is related to the article titled "Aberration correction in long GRIN lens-based microendoscopes for extended field-of-view two-photon imaging in deep brain regions".

Authors: 

Andrea Sattin^1,2,*, Chiara Nardin^1,2,*, Simon Daste³, Monica Moroni^2,4, Innem Reddy⁵, Carlo Liberale⁵, Stefano Panzeri^2,6, Alexander Fleischmann³, Tommaso Fellin^1,2,#

^*equal contribution; ^#corresponding author: tommaso.fellin@iit.it

Affiliations:

¹Optical Approaches to Brain Function Laboratory, Istituto Italiano di Tecnologia, Genova, Italy

²Neural Coding Laboratory, Istituto Italiano di Tecnologia, Genova and Rovereto, Italy

³Department of Neuroscience and Carney Institute for Brain Science, Brown University, Providence, USA

⁴Neural Computation Laboratory, Center for Neuroscience and Cognitive Systems @UniTn, Istituto Italiano di Tecnologia, Rovereto, Italy

⁵Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia

⁶Institute for Neural Information Processing, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany

DOI: https://doi.org/10.7554/eLife.101420.3

Description:

Data contained in this dataset were used to generate Figure 5,6 and figure supplements 1,2 related to Figure 6. Data are synthetic calcium t-series (tiff files) simulating the activity of neuronal populations virtually sampled using the 6.4 mm-long uncorrected microendoscope.  

We generated synthetic calcium t-series to evaluate the impact of the improved optical performance of long aberration corrected microendoscopes on the ability to extract information about neuronal activity. 

To build synthetic calcium data, we first generated neurons with 3D distribution and anatomical properties (i.e., cell size and cell density) similar to those measured in the mouse olfactory cortex, the ventral brain region which we imaged in vivo, and the biophysical characteristics of one of the two indicators used in our experiments, jGCaMP8f. We then simulated the optical sampling of 3D volume of neurons with the point spread function (PSF) properties of the uncorrected and corrected microendoscopes previously characterized. Fluorescence signals integrated over the PSF volume were then projected on a 2D matrix of pixels in time, with a frequency of 30 Hz, to obtain synthetic t-series (duration: 5 min).