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Tools, algorithms, and frameworks for managing and analyzing neural data.

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awesome-neural-data-tools

Tools, algorithms, and frameworks for managing and analyzing neural data (derived from original notes from the 2018 BRAIN Initiative Investigators Meeting by Liam Paninski)

Calcium+voltage imaging:

Spike sorting:

Optogenetic stimulation

Behavioral + stimulus control (and analysis)

Fluorescence Imaging

Compression

Registration & stitching

Electron microscopy

scRNAseq / FISH

Eye tracking

Animal part tracking

Statistical Machine Learning

Spike train data analysis methods - encoding models, decoders, dimensionality reduction, etc

Visualization (2D, 3D, 4D, 5D)

Web-Viz

Local-Viz

Pipelines, data sharing, reproducibility

Tracking provenance of data / analysis outputs. Automatic repopulation of databases as analysis algorithms are updated. Store both data and model simulation output

Data specifications

Reproducibility + knowledge sharing tools

Data/Tool Repositories:

Review articles

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Tools, algorithms, and frameworks for managing and analyzing neural data.

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