Biology subjects

Gauthier, J. L.

Publications and source records attributed to Gauthier, J. L..

2 recordsLinked to original sources

bioRxiv2018

CaImAn: An open source tool for scalable Calcium Imaging data Analysis

Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. Here we present CaImAn, an open-source library for calcium imaging data analysis. CaImAn provides automatic and scalable methods to address problems common to pre-processing, including motion correction, neural activity identification, and registration across different sessions of data collection. It does this while requiring minimal user intervention, with good performance on computers ranging from laptops to high-performance computing clusters. CaImAn is suitable for two-photon and one-photon imaging, and also enables real-time analysis on streaming data. To benchmark the performance of CaImAn we collected a corpus of ground truth annotations from multiple labelers on nine mouse two-photon datasets. We demonstrate that CaImAn achieves near-human performance in detecting locations of active neurons.

neuroscience↗

bioRxiv2017

Context-invariant encoding of reward location in a distinct hippocampal population

The hippocampus plays a critical role in goal-directed navigation. Across different environments, however, the hippocampal map seems to be randomized, making it unclear how goal locations might be encoded. To address this question, we trained mice to seek reward at several locations on virtual linear tracks, and optical recordings of calcium activity were made at cellular resolution from two major hippocampal output structures, CA1 and the subiculum. These experiments revealed a population of neurons that were consistently active near reward locations. Their pattern of activity sharply contrasted with simultaneously-recorded place cells and even persisted across environments, when other cells remapped randomly. Their timing was closely correlated with reward anticipation behaviors, yet could not be explained by the behaviors themselves, raising the possibility that reward-associated cell signals were used by mice to identify the reward location. These results demonstrate that the hippocampus employs a context-invariant marker of goal locations, and reveal a novel target for studying how the hippocampus contributes to navigation.

neuroscience↗