old.txt

| | Format | Description | Citation | Modality(s) |
| :--- | :--- | :--- | :--- | :--- |
| 1 | **[EDF, EDF+](https://www.edfplus.info/)** | An early standardized data format used for sleep recordings (EEG, respiration, EMG, etc.). Files include a header record with subject info, time, and signal identification. | (Kemp et al., 1992; Kemp and Olivan 2003) | Electrophysiology |
| 2 | **[MEF](https://github.com/msel-lab/mef-v3)** | Open-source software for high-volume neural data. Features range encoding for compression, 128-bit encryption for patient security, and redundancy checks. | (Brinkmann et al., 2009) | Electrophysiology |
| 3 | **[Orca](https://github.com/AllenInstitute/borg)** | Also known as BORG; developed by the Allen Institute for electrophysiology and optophysiology data. It is built upon the HDF5-based format. | (Godfrey, 2014; Friedsam, 2016) | Electrophysiology |
| 4 | **[KWIK](https://github.com/klusta-team/kwik)** | Part of the Klusta suite for spike sorting. These HDF5-based files store spike times, clusters, and associated metadata. | (Kadir et al., 2014) | Electrophysiology |
| 5 | **[NEO](https://neuralensemble.org/neo/)** | Successor to Neuroshare API; provides a design specification for core neuroscience objects to decouple data representation from downstream analysis. | (Garcia et al., 2014) | Electrophysiology |
| 6 | **[BRAINformat](https://github.com/oruebel/brainformat)** | An open-source library defining application-independent design concepts using HDF5 to create a general framework for scientific data standardization. | (Rübel et al., 2016) | Electrophysiology |
| 7 | **[ONE](https://github.com/int-brain-lab/ONE)** | Developed by the IBL consortium for multi-lab sharing. Uses an `object.attribute.extension` naming scheme compatible across various file formats. | (IBL et al., 2023) | Electrophysiology, Imaging, Other |
| 8 | **[NWB](https://www.nwb.org/)** | A common standard for sharing and archiving neurophysiology data, including intracellular/extracellular electrophysiology, optical physiology, and behavior. | (Teeters et al., 2015; Rubel et al., 2022) | Electrophysiology, Other |
| 9 | **[DICOM](https://www.dicomstandard.org/)** | The international standard for medical imaging (MRI, CT, X-ray). Defines formats for clinical data exchange and quality across radiology and cardiology. | (NEMA, 1993) | Imaging |
| 10 | **[NIFTI](https://nifti.nimh.nih.gov/)** | Designed specifically for brain imaging; packages image data and metadata into a single file to simplify sharing and neuroimaging analysis. | (Cox et al., 2004) | Imaging |
| 11 | **[NIX](https://github.com/G-Node/nix)** | A hierarchical and extensible format designed to store diverse data including electrophysiology, imaging, and behavioral datasets. | (Martone 2014) | Imaging |
| 12 | **[BIDS](https://bids.neuroimaging.io/)** | A standard for organizing and describing neuroimaging (and later EEG) data to promote reproducibility and interoperability across labs and tools. | (Gorgolewski et al., 2016) | Imaging |


| | Package | Description | Citation | Language |
| :--- | :--- | :--- | :--- | :--- |
| 1 | **[Pynapple](https://github.com/PeyracheLab/pynapple)** | A lightweight python package designed to process a broad range of time-resolved data in systems neuroscience, which facilitates analysis through data objects and methods that have the potential to simplify data analysis for neural and behavioral data types. | (Viejo et al. 2023) | Python |
| 2 | **[Spyglass](https://github.com/LorenFrankLab/spyglass)** | An open-source, python based data analysis framework that facilitates the storage, analysis, visualization, and sharing of neuroscience data towards more reproducible research | (Lee and Denovellis et al. 2024) | Python |
| 3 | **[Neurodsp](https://github.com/neurodsp-tools/neurodsp)** | A python-based software package specifically designed to be used for analyzing neural time series data and their time-varying properties | (Cole et al., 2019) | Python |
| 4 | **[GhostiPy](https://github.com/kemerelab/ghostipy)** | A python-based open source software toolbox with implementations of various signal processing and spectral analyses, and prioritizes performance and efficiency through the use of parallelized algorithms | (Chu & Kemere. 2021) | Python |
| 5 | **[bctpy](https://github.com/aestrivex/bctpy)** | Implements many graph theoretical measures to analyze brain activity | (LaPlante, 2013) | Python |
| 6 | **[natverse](https://natverse.org/)** | An R-based suite of toolboxes to perform popular analysis of neuroanatomical data | (Bates et al., 2020) | R |
| 7 | **[NetworkToolbox](https://cran.r-project.org/web/packages/NetworkToolbox/index.html)** | Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. | (Alexander 2018) | R |
| 8 | **[LZeroSpikeInference](https://cran.r-project.org/web/packages/LZeroSpikeInference/index.html)** | A collection of algorithms to determine the exact time at which a neuron spikes on the basis of its fluorescence trace using an L0 penalty. | (Jewell & Witten 2017) | R |
| 9 | **[Brain Connectivity Toolbox](https://sites.google.com/site/bctnet/)** | A popular toolbox used for complex brain-network analysis. | (Rubinov M, Sporns O 2010) | MATLAB |
| 10 | **[Syntropy](https://github.com/thosvarley/syntropy)** | A python library for multivariate information theoretic analysis of discrete and continuous data | (Varley 2025) | Python |
| 11 | **[Cascade](https://github.com/HelmchenLabSoftware/Cascade)** | Cascade translates calcium imaging ΔF/F traces into spiking probabilities or discrete spikes using deep networks | (Rupprecht et al., 2021) | Python |
| 12 | **[BSD](https://github.com/jertubiana/BSD)** | Blind Sparse Deconvolution for inferring spike trains from fluorescence recordings. | (Tubiana et al., 2020) | MATLAB |
| 13 | **[Chronux](http://chronux.org/)** | Open-source software package for the analysis of neural data for both point process and continuous data, ranging from preprocessing, exploratory and confirmatory analysis | (Mitra & Bokil, 2008) | MATLAB |


| | Repository | Description | Citation | Discipline |
| :--- | :--- | :--- | :--- | :--- |
| 1 | **[CRCNS](https://crcns.org/)** | A result of a NSF/NIH sponsored collaborative research program, CRCNS is a public archive that shares experimental neuroscience data. | Teeters et al., 2008 | Neuroscience |
| 2 | **[DANDI](https://dandiarchive.org/)** | The DANDI archive is a cloud-based repository for sharing and publishing electrophysiology data, including cellular and systems-level recordings. | Gosh et al., 2023 | Neuroscience |
| 3 | **[NeMO](https://nemoarchive.org/)** | The NeMO repository is the access point for genomic data from brain-related research projects. Primary repository for the BRAIN initiative. | [nemoarchive.org](https://nemoarchive.org) | Neuroscience |
| 4 | **[OpenNeuro](https://openneuro.org/)** | A free and open platform for sharing MRI, MEG, EEG, iEEG, and other neuroimaging datasets, organized according to the BIDS standard. | Markiewicz et al., 2021 | Neuroscience |
| 5 | **[DABI](https://dabi.loni.usc.edu/)** | A data repository and portal for projects that collect human and animal intracranial recordings. Serving as a main repository for BRAIN Initiative data. | Duncan et al., 2023 | Neuroscience |
| 6 | **[EBRAINS](https://www.ebrains.eu/)** | EBRAINS provides access to a free and open database of neuroscience data, computational models and software. | [ebrains.eu](https://www.ebrains.eu) | Neuroscience |
| 7 | **[Dryad](https://datadryad.org/)** | A data publishing platform committed to the open availability and routine re-use of research data under a Creative Commons Public Domain License. | [datadryad.org](https://datadryad.org/) | Multiple |
| 8 | **[Zenodo](https://zenodo.org/)** | Designed by CERN, Zenodo provides long-term preservation of digital objects for high-energy physics and many other disciplines. | [zenodo.org](https://zenodo.org/) | Multiple |
| 9 | **[Figshare](https://figshare.com/)** | A freely available data publishing platform where researchers can share and receive credit for multiple types of scholarly output. | [figshare.com](https://figshare.com/) | Multiple |
| 10 | **[OSF](https://osf.io/)** | A free and open-source project management tool that supports researchers throughout their entire project lifecycle in open science. | [osf.io](https://osf.io/) | Multiple |
| 11 | **[Vivli](https://vivli.org/)** | A global data sharing and analytics platform focusing on individual participant-level data from completed clinical trials. | [vivli.org](https://vivli.org/) | Multiple |
| 12 | **[Allen Brain Map](https://portal.brain-map.org/)** | Integrated suite of gene expression, connectivity, and neuroanatomical data for human and mouse brains, including the 3D Common Coordinate Framework (CCF). | Lein et al., 2007 | Neuroscience |
| 13 | **[Human Connectome Project](https://www.humanconnectome.org/)** | Resource for high-quality neuroimaging data (structural/functional MRI, MEG, EEG) from large cohorts across the lifespan. | Van Essen et al., 2013 | Neuroscience |
| 14 | **[NeuroMorpho.org](https://neuromorpho.org/)** | The largest inventory of digitally reconstructed neurons and glia, providing over 150,000 neuronal morphologies. | Ascoli et al., 2007 | Neuroscience |
| 15 | **[FCP-INDI](https://fcon_1000.projects.nitrc.org/)** | Consortium dedicated to sharing resting-state fMRI and related phenotypic data, including the ABIDE and ADHD-200 datasets. | Mennes et al., 2013 | Neuroscience |
| 16 | **[MouseLand](https://github.com/MouseLand)** | Provides ground truth training datasets and tools (like Suite2p and Cellpose) for calcium imaging and cellular segmentation. | Stringer & Pachitariu, 2019 | Neuroscience |
| 17 | **[NIMH Data Archive (NDA)](https://nda.nih.gov/)** | Infrastructure storing data from hundreds of human mental health research studies, including the ABCD Study. | NIMH, 2023 | Neuroscience |