Analysis and Visualization Tools

NWB Widgets

A library of widgets for visualizing NWB data in a Jupyter notebook (or lab). The widgets make it easy to navigate through the hierarchical structure of the NWB file and visualize specific data elements.

Neurosift

Interactive neuroscience visualizations in the browser. Neurosift caters to both individual users through its local mode, allowing the visualization of views directly from your device, as well as a remote access function for presenting your findings to other users on different machines.

NWB Explorer

A web application developed by MetaCell for reading, visualizing and exploring the content of NWB 2 files. The portal comes with built-in visualization for many data types, and provides an interface to a jupyter notebook for custom analyses and open exploration.

HDF Tools

A broad range of useful tools for inspecting and browsing HDF5 files, including HDFView, HDF5 plugins for Jupyter or VSCode, and command-line tools.

SpikeInterface

A collection of Python modules designed to improve the accessibility, reliability, and reproducibility of spike sorting and all its associated computations.

CellExplorer

A graphical user interface (GUI), a standardized processing module and data structure for exploring and classifying single cells acquired using extracellular electrodes.

EcogVIS

A Python-based, time series visualizer for Electrocorticography (ECoG) signals stored in NWB files. Makes it intuitive and simple to visualize ECoG signals from selected channels, brain regions, make annotations and mark intervals of interest.

Neo

A Python package for working with electrophysiology data in Python, together with support for reading and writing a wide range of neurophysiology file formats.

EEGLAB

A MATLAB-based electrophysiology (ECoG/iEEG/EEG) software to process and visualize data stored in NWB files.

CaImAn

A computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

Suite2p

An imaging processing pipeline written in Python, including modules for Registration, Cell detection, Spike detection, and a Visualization GUI.

CIAtah

A Matlab software package for analyzing one- and two-photon calcium imaging datasets (formerly calciumImagingAnalysis).

EXTRACT

A Tractable and Robust Automated Cell extraction Tool for calcium imaging, which extracts the activities of cells as time series from both one-photon and two-photon Ca2+ imaging movies.

CICADA

A Python pipeline providing a graphical user interface (GUI) that allows the user to visualize, explore and analyze Calcium Imaging data contained in NWB files.

OptiNiSt

A GUI based workflow pipeline tool for processing two-photon calcium imaging data (Optical Neuroimage Studio).

GraFT

A signal extraction method for spatio-temporal data, using a diffusion map to learn a graph over spatial pixels that enables stochastic filtering of learned sparse representations.

PatchView

A GUI tool to perform data analysis and visualization on multi channel whole-cell recording (multi-patch) data, including firing pattern analysis, mini-event analysis, synaptic connection detection, and morphological analysis.

DeepLabCut

An efficient method for 2D and 3D markerless pose estimation based on transfer learning with deep neural networks that achieves excellent results with minimal training data.

SLEAP

An open source deep-learning based framework for multi-animal pose tracking, capable of tracking any type or number of animals with an advanced labeling/training GUI for active learning and proofreading.

CEBRA

A machine-learning method that can compress time series to reveal hidden structures in data variability, excelling with behavioral and neural data recorded simultaneously.

Pynapple

A unified toolbox for integrated analysis of multiple data sources, designed to be 'plug & play' with support for electrophysiology, calcium imaging, and motion capture data.

Spyglass

A framework for building analysis workflows with a focus on reproducibility and sharing, using NWB and DataJoint to manage data and build pipelines.

DANDI

The NIH BRAIN Initiative archive for publishing and sharing neurophysiology data including electrophysiology, optophysiology, behavioral time-series, and images from immunostaining experiments.

DataJoint

An open-source project for defining and operating computational data pipelines—sequences of steps for data acquisition, processing, and transformation.