Data Analysis

When meta-research (research on research) makes an observation or points out a problem (such as a flaw in methodology), the project should be repeated later to determine whether the problem remains.

A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning. Project Author(s) Harry Carey, Michael Pegios; Lewis Martin; Chris Saleeba; Anita J.

BORIS is an easy-to-use event logging software for video/audio coding and live observations. Project Author(s) Olivier Friard; Marco Gamba Project Links www.boris.unito.it This post was automatically generated by anonymous

This repository contains the code of the Neuronal Spike Shapes (NSS), a simple approach for analyzing the electrophysiological profiles of cells based on their Action Potential (AP) waveforms. The NSS method explores the heterogeneity of cell types and states by summarizing the AP waveform into a triangular representation complemented by a set of derived electrophysiological (EP) features.

Movement is a a Python toolbox for analysing body movements across space and time, to aid the study of animal behaviour in neuroscience. Pose estimation tools, such as DeepLabCut and SLEAP are now commonplace when processing video data of animal behaviour.

NeuroMatic is a collection of WaveMetrics Igor Pro software tools for acquiring, analyzing and simulating electrophysiological data. By merging a wide range of tools into a single package, NeuroMatic facilitates a more integrated style of research.

DataJoint Elements is a growing compilation of community-curated, open-source software modules for building automated data pipelines and analysis workflows for neuroscience experiments. DataJoint Elements enables: Secure tracking of animal subjects, equipment, and procedures Automatic data ingestion Customized research workflows Faster deployment Improved reproducibility Greater continuity across projects Secure tracking.

DataJoint Core is an open-source toolkit for defining and operating computational data pipelines (i.e., sequences of steps for data acquisition, processing, and transformation). Pipelines built in DataJoint Core offer: Efficient design with intuitive queries Automated, reproducible computation with full referential integrity Coordination of multiple human and computer workers Flexibility to adapt and change DataJoint Core includes libraries for Python and MATLAB, a REST API, and GUI tools for data entry and visualizations.

SqueakR is an open-source R package, available on CRAN, which streamlines bioacoustics research through automated data processing and visualizations for rodent vocalizations exported from DeepSqueak. These functions are harnessed through the ‘SqueakR’ Shiny Dashboard, available as a function within the package, which can be used to visualize experimental results and analyses, as well as conduct statistical significance test between call features across groups.

Climbing fiber inputs to Purkinje cells provide instructive signals critical for cerebellum-dependent associative learning. Studying these signals in head-fixed mice facilitates the use of imaging, electrophysiological, and optogenetic methods. Here, a low cost behavioral platform (~$1000) was developed that allows tracking of associative learning in head-fixed mice that locomote freely on a running wheel.