This is a list of tools we are cataloging as a convenience reference for NWB:N users. This is not a comprehensive list of NWB:N tools. Many of these tools are built and supported by other groups, and are in active development.
Spikeinterface is a collection of Python modules designed to improve the accessibility, reliability, and reproducibility of spike sorting and all its associated computations.
With SpikeInterface, users can:
- read/write many extracellular file formats.
- pre-process extracellular recordings.
- run many popular, semi-automatic spike sorters.
- post-process sorted datasets.
- compare and benchmark spike sorting outputs.
- validate and curate spike sorting outputs.
- visualize recordings and spike sorting outputs.
NWB Explorer is 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.
Cell detection in calcium imaging recordings. suite2p includes the following modules:
- Cell detection
- Spike detection
- Visualization GUI
Software package for analyzing one- and two-photon calcium imaging datasets.
- Includes a GUI to allow users to do large-scale batch analysis, accessed via the repository’s
- The underlying functions can also be used to create GUI-less, command line-ready analysis pipelines.
- Includes code for determining animal position (e.g. in open-field assay).
- Supports Neurodata Without Borders data standard for cell-extraction (e.g. outputs of PCA-ICA, CNMF, etc.).
Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization. CaImAn now supports reading and writing data in NWB 2.0. NWB tutorial here.
Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology built in Matlab and Java. Brainstorm now supports the NWB data format for importing ECoG and invasive electrophysiology data. The application provides a graphical interface for a preprocessing and analysis pipeline, including spike sorting using WaveClus, UltraMegaSort2000, KiloSort or Klusters, a large suite of spiking and LFP analyses, data visualization, and interactive visualization of anatomical topographies.
NWBwidgets is a library for exploring an NWB file in a Jupyter notebook. This tool lets you traverse the hierarchical structure of an NWB file and visualize the data from each of the NWB elements within the file.
EcogVIS is a Python-based, time series visualizer for Electrocorticography (ECoG) signals stored in NWB files. EcogVIS makes it intuitive and simple to visualize ECoG signals from selected channels, brain regions, make annotations and mark intervals of interest. Signal processing and analysis tools will soon be added.
Disclaimer: Reference herein to any specific product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not constitute or imply its endorsement, recommendation, or favoring by the NWB:N development team, United States Government or any agency thereof, or The Regents of the University of California. Use of the NeurodataWithoutBorders name for endorsements is prohibited.