Vobi One: a data processing software package for functional optical imaging.
Optical imaging is the only technique that allows to record the activity of a neuronal population at the mesoscopic scale. A large region of the cortex (10-20 mm diameter) is directly imaged with a CCD camera while the animal performs a behavioral task, producing spatio-temporal data with an unprecedented combination of spatial and temporal resolutions (respectively, tens of micrometers and milliseconds). However, researchers who have developed and used this technique have relied on heterogeneous software and methods to analyze their data. In this paper, we introduce Vobi One, a software package entirely dedicated to the processing of functional optical imaging data. It has been designed to facilitate the processing of data and the comparison of different analysis methods. Moreover, it should help bring good analysis practices to the community because it relies on a database and a standard format for data handling and it provides tools that allow producing reproducible research. Vobi One is an extension of the BrainVISA software platform, entirely written with the Python programming language, open source and freely available for download at https://trac.int.univ-amu.fr/vobi_one.
Institut de Neurosciences de la Timone UMR 7289, CNRS - Aix Marseille Université Marseille, France.
Sylvain
S
Takerkart
Institut de Neurosciences de la Timone UMR 7289, CNRS - Aix Marseille Université Marseille, France ; LabISEN, Vision Department, Institut Supérieur de lElectronique et du Numérique Brest, France.
Philippe
P
Katz
Institut de Neurosciences de la Timone UMR 7289, CNRS - Aix Marseille Université Marseille, France.
Flavien
F
Garcia
Institut de Neurosciences de la Timone UMR 7289, CNRS - Aix Marseille Université Marseille, France.
Sébastien
S
Roux
McGill Vision Research, Department of Ophtalmology, McGill University Montréal, QC, Canada.
Alexandre
A
Reynaud
Institut de Neurosciences de la Timone UMR 7289, CNRS - Aix Marseille Université Marseille, France.
Frédéric
F
Chavane
linear model; neuroscience; optical imaging; python; signal processing