catalystneuro/roiextractors

Python-based module for extracting from, converting between, and handling optical imaging data from several file formats. Inspired by SpikeInterface.

Language: Python - Size: 22.9 MB - Last synced at: about 19 hours ago - Pushed at: about 22 hours ago - Stars: 15 - Forks: 10

catalystneuro/download-dash

Language: Python - Size: 1.44 MB - Last synced at: about 23 hours ago - Pushed at: 1 day ago - Stars: 0 - Forks: 0

catalystneuro/dandi-annotations

Language: Python - Size: 5.86 KB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

catalystneuro/kind-lab-to-nwb

NWB Conversion project for the Kind lab.

Language: Jupyter Notebook - Size: 3.71 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 1 - Forks: 2

catalystneuro/hdmf Fork of hdmf-dev/hdmf

The Hierarchical Data Modeling Framework

Language: Python - Size: 9.18 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 0 - Forks: 0

catalystneuro/surmeier-lab-to-nwb

Language: Python - Size: 1.56 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 0 - Forks: 0

catalystneuro/neuroconv

Create NWB files by converting and combining neural data in proprietary formats and adding essential metadata.

Language: Python - Size: 701 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 61 - Forks: 27

catalystneuro/catalystneuro-dendro-apps

CatalystNeuro Dendro Apps

Language: Python - Size: 48.8 KB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0

catalystneuro/schwerdt-lab-to-nwb

NWB Conversion project for the Schwerdt lab at University of Pittsburgh.

Language: Python - Size: 62.5 KB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0

catalystneuro/access-page Fork of dandi/access-page

Visualizations of data usage across the archive.

Size: 14.7 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 0 - Forks: 0

catalystneuro/schneider-lab-to-nwb

Language: Jupyter Notebook - Size: 19.1 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 0 - Forks: 1

catalystneuro/ndx-ophys-devices

This is an NWB extension for storing metadata of devices used in optical experimental setup (microscopy, fiber photometry, optogenetic stimulation etc.)

Language: Python - Size: 81.1 KB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 1 - Forks: 0

catalystneuro/dan-lab-to-nwb

Language: Python - Size: 121 KB - Last synced at: 20 days ago - Pushed at: 21 days ago - Stars: 0 - Forks: 0

catalystneuro/hdmf-zarr Fork of hdmf-dev/hdmf-zarr

Zarr I/O backend for HDMF

Language: Python - Size: 3.66 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 0 - Forks: 0

catalystneuro/example-notebooks Fork of dandi/example-notebooks

Language: Jupyter Notebook - Size: 64.8 MB - Last synced at: 30 days ago - Pushed at: 30 days ago - Stars: 0 - Forks: 0

catalystneuro/IBL-to-nwb

Conversion of IBL data to NWB format.

Language: Python - Size: 14.1 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 3 - Forks: 5

catalystneuro/jadhav-lab-to-nwb

Language: Python - Size: 635 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

catalystneuro/ndx-binned-spikes

NWB extension to store binned spikes (e.g. a non averaged PSTH) with respect to an time events

Language: Python - Size: 87.9 KB - Last synced at: 12 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

catalystneuro/ecogVIS

Time series visualizer and data processing tools for Electrocorticography (ECoG) signals stored in NWB files, for Python.

Language: Python - Size: 30.8 MB - Last synced at: 17 days ago - Pushed at: about 1 year ago - Stars: 25 - Forks: 18

catalystneuro/lazy_ops

Lazy transposing and slicing of h5py and Zarr Datasets

Language: Python - Size: 72.3 KB - Last synced at: 18 days ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 5

catalystneuro/ndx-fiber-photometry

This is an NWB extension for storing fiber photometry recordings and associated metadata.

Language: Python - Size: 113 KB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 3 - Forks: 0

catalystneuro/cohen-u01-to-nwb

Language: Python - Size: 2.16 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

catalystneuro/ndx-microscopy

An enhancement to core NWB schema types related to microscopy data.

Language: Python - Size: 301 KB - Last synced at: 24 days ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

catalystneuro/python-neo Fork of NeuralEnsemble/python-neo

Neo is a package for representing electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats

Language: Python - Size: 109 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0

catalystneuro/ndx-vame

NWB extension for VAME.

Language: Python - Size: 5.31 MB - Last synced at: about 1 month ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

catalystneuro/mcp_read_images

Language: JavaScript - Size: 1.6 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 7 - Forks: 1

catalystneuro/agents

Open Neuroscience Agents

Language: Python - Size: 95.7 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 2 - Forks: 1

catalystneuro/pynwb Fork of NeurodataWithoutBorders/pynwb

A Python API for working with Neurodata stored in the NWB Format

Language: Python - Size: 44.9 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

catalystneuro/nwbinspector Fork of NeurodataWithoutBorders/nwbinspector

Tool to help inspect NWB files for compliance with NWB Best Practices

Language: Python - Size: 2.67 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

catalystneuro/spikeinterface Fork of SpikeInterface/spikeinterface

A Python-based module for creating flexible and robust spike sorting pipelines.

Language: Python - Size: 70.5 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

catalystneuro/cookiecutter-my-lab-to-nwb-template

The standard cookiecutter template for all lab-specific NWB conversions.

Language: Python - Size: 103 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 1

catalystneuro/staged-extensions Fork of nwb-extensions/staged-extensions

A place to submit NWB Extensions for registration in the official NDX Catalog

Size: 296 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

catalystneuro/khaliq-lab-to-nwb

Language: Python - Size: 14.6 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

catalystneuro/ndx-pose Fork of rly/ndx-pose

NWB extension to store pose estimation data

Language: Python - Size: 138 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

catalystneuro/hnasko-lab-to-nwb

NWB Conversion project for the Hnasko Lab

Language: Python - Size: 454 KB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 0 - Forks: 0

catalystneuro/pagan-lab-to-nwb

NWB Conversion project for the Pagan lab.

Language: Python - Size: 326 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

catalystneuro/ndx-sound

NWB extension of sounds

Language: Python - Size: 1.77 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

catalystneuro/neuroconv-spyglass

Central Repository for spyglass-compatible interfaces and custom nwb-to-spyglass insertion code

Language: Python - Size: 17.6 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

catalystneuro/photon-flux-estimation

A Python library for estimating photon flux from multiphoton imaging data. This package provides tools to compute photon sensitivity and generate photon flux visualizations from imaging data.

Language: Python - Size: 58.4 MB - Last synced at: about 2 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

catalystneuro/cai-lab-to-nwb

NWB Conversion project for the Cai lab

Language: Jupyter Notebook - Size: 5.63 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

catalystneuro/dicarlo-lab-to-nwb

Language: Python - Size: 1.99 MB - Last synced at: 2 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 1

catalystneuro/constantinople-lab-to-nwb

NWB Conversion project for the Constantinople lab at NYU Center for Neural Science.

Language: Jupyter Notebook - Size: 3.79 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

catalystneuro/mcp

CatalystNeuro MCP servers

Language: Python - Size: 82 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

catalystneuro/git2rag

Smart and efficient embedding of your Github repository contents

Language: Python - Size: 123 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

catalystneuro/dandi.github.io Fork of dandi/dandi-about

Website code for DANDI Project

Language: SCSS - Size: 31.4 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

catalystneuro/catalystneuro.github.io_old Fork of mmistakes/minimal-mistakes

Language: TypeScript - Size: 201 MB - Last synced at: 14 days ago - Pushed at: 7 months ago - Stars: 0 - Forks: 1

catalystneuro/cn-website

Language: TypeScript - Size: 129 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

catalystneuro/nelson-lab-to-nwb

Language: Jupyter Notebook - Size: 33.2 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

catalystneuro/dandi-hugo-example

example of website using hugo

Language: HTML - Size: 5.31 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

catalystneuro/dandi-docusaurus-example

example of website using docusaurus

Language: TypeScript - Size: 854 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

catalystneuro/ndx-anatomical-localization

Language: Python - Size: 47.9 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 1

catalystneuro/ndx-hierarchical-behavioral-data

Language: Python - Size: 231 KB - Last synced at: 22 days ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 2

catalystneuro/nwb-website Fork of davewibisono/nwb

Size: 50.8 MB - Last synced at: 2 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 1

catalystneuro/leifer_lab_to_nwb

Conversion scripts for the Leifer lab. Includes the publication Neural signal propagation atlas of Caenorhabditis elegans (Nature, 2023).

Language: Python - Size: 125 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

catalystneuro/buzsaki-lab-to-nwb

Language: Python - Size: 5.76 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 1

catalystneuro/higley-lab-to-nwb

NWB Conversion project for the Higley lab

Language: Python - Size: 10.9 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

catalystneuro/.github

Company-wide documentation of practices, protocols, policies, and processes.

Size: 65.4 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

catalystneuro/ndx-subjects

An NWB extension for custom species metadata.

Language: Python - Size: 12.7 KB - Last synced at: 27 days ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

catalystneuro/ndx-photometry Fork of akshay-jaggi/ndx-photometry

photometry extension for nwb

Language: Python - Size: 313 KB - Last synced at: 2 days ago - Pushed at: 11 months ago - Stars: 0 - Forks: 1

catalystneuro/reimer-arenkiel-lab-to-nwb

Reimer-Arenkiel lab conversion to NWB

Language: Python - Size: 2.18 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

catalystneuro/ndx-miniscope

Neurodata Without Borders extension for metadata relevant for miniscope acquisition

Language: Python - Size: 113 KB - Last synced at: 8 days ago - Pushed at: 12 months ago - Stars: 3 - Forks: 1

catalystneuro/tqdm_publisher

Subscribe to updates from tqdm progress bars with arbitrary callback functions.

Language: Python - Size: 110 KB - Last synced at: 26 days ago - Pushed at: 4 months ago - Stars: 2 - Forks: 1

catalystneuro/jazayeri-lab-to-nwb

Collection of tools and scripts for converting data from the Jazayeri lab to NWB format.

Language: Python - Size: 282 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 1

catalystneuro/tye-lab-to-nwb

NWB Conversion project for the Tye lab at the Salk Institute.

Language: Python - Size: 193 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

catalystneuro/visual-coding-to-nwb-v2

Conversion of old v1 NWB files from https://registry.opendata.aws/allen-brain-observatory/ to v2 so they can be uploaded to DANDI.

Language: Python - Size: 6.8 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

catalystneuro/shenoy-lab-to-nwb

Language: Python - Size: 377 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 1 - Forks: 0

catalystneuro/dombeck-lab-to-nwb

NWB Conversion project for the Dombeck lab at Northwestern University.

Language: Jupyter Notebook - Size: 10.3 MB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

catalystneuro/ndx-depth-moseq Fork of pauladkisson/ndx-depth-moseq

Language: Python - Size: 77.1 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

catalystneuro/ndx-extracellular-channels

Language: Python - Size: 20.5 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

catalystneuro/nwb-conversion-tools 📦

Create NWB files by converting and combining neural data in proprietary formats and adding essential metadata.

Language: Python - Size: 11.1 MB - Last synced at: 20 days ago - Pushed at: over 2 years ago - Stars: 25 - Forks: 12

catalystneuro/ndx-patterned-ogen

patterned (holographic) optogenetic extension to NWB standard

Language: Jupyter Notebook - Size: 456 KB - Last synced at: 24 days ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

catalystneuro/GuPPy Fork of LernerLab/GuPPy

Guided Photometry Analysis in Python, a free and open-source FP analysis tool.

Language: Python - Size: 23.8 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

catalystneuro/nwb_hackathons Fork of NeurodataWithoutBorders/nwb_hackathons

Repository for collecting materials from nwb hackathons

Language: Jupyter Notebook - Size: 366 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

catalystneuro/format-support-table

A summary of format support in the NWB ecosystem

Language: JavaScript - Size: 266 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1

catalystneuro/howe-lab-to-nwb

NWB Conversion project for the Howe lab at Boston University.

Language: Python - Size: 24.4 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

catalystneuro/stratneuro_2024

Material for StratNeuro 2024 workshop

Language: Jupyter Notebook - Size: 22.5 MB - Last synced at: 9 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1

catalystneuro/lerner-lab-to-nwb

Language: Python - Size: 288 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

catalystneuro/raw_s3_log_parser

Parse raw S3 logs.

Language: Python - Size: 16.6 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

catalystneuro/si-dendro-apps

SpikeInterface Apps for Dendro

Language: Python - Size: 153 KB - Last synced at: 4 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

catalystneuro/ontology-matching-service

Ontology matching service based on LLMs for facilitating the extraction of scientific metadata from ontologies

Language: Jupyter Notebook - Size: 1.04 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0

catalystneuro/turner-lab-to-nwb

NWB Conversion project for the Turner lab at the University of Pittsburgh.

Language: Python - Size: 1.12 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

catalystneuro/wormdatamodel Fork of leiferlab/wormdatamodel

Data model for whole brain recordings

Size: 543 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

catalystneuro/catalystneuro-website Fork of davewibisono/catalyst-neuro

Language: HTML - Size: 56.6 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

catalystneuro/datta-lab-to-nwb

Language: Python - Size: 365 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 2

catalystneuro/movshon-lab-to-nwb

Language: Jupyter Notebook - Size: 4.78 MB - Last synced at: 28 days ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

catalystneuro/ndx-facemap-motionsvd

extension to store the motion SVD output from FaceMap software

Language: Python - Size: 38.1 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

catalystneuro/dandiset-search-service

Language: Jupyter Notebook - Size: 5.42 MB - Last synced at: 9 months ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0

catalystneuro/ODIN-23-summary-paper

A social commentary paper summarizing the ODIN 2023 symposium and its discussions.

Size: 161 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

catalystneuro/ndx-aind-metadata

Language: Python - Size: 24.4 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

catalystneuro/ndx-turner-metadata

The NWB extension for storing Turner lab specific metadata

Language: Python - Size: 28.3 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

catalystneuro/json-schema-to-dash-forms

JSON schema to Dash forms

Language: Python - Size: 380 KB - Last synced at: 26 days ago - Pushed at: almost 2 years ago - Stars: 10 - Forks: 3

catalystneuro/mousev1-to-nwb

NWB Conversion project for the Adesnik lab at UC Berkeley.

Language: Python - Size: 17.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

catalystneuro/fparse Fork of r1chardj0n3s/parse 📦

Parse strings using a specification based on the Python format() syntax.

Language: Python - Size: 345 KB - Last synced at: 7 days ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

catalystneuro/spiketoolkit Fork of SpikeInterface/spiketoolkit

Python-based tools for pre-, post-processing, validating, and curating spike sorting datasets.

Language: Python - Size: 3.85 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

catalystneuro/pyintan Fork of alejoe91/pyintan

Python reader for INTAN rhs files

Language: Python - Size: 61.5 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

catalystneuro/handbook Fork of dandi/handbook

Handbook for interacting with the DANDI archive.

Size: 3.69 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

catalystneuro/oconnor-lab-to-nwb

Language: Python - Size: 88.9 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

catalystneuro/buffalo-lab-to-nwb

Scripts to convert Buffalo Lab data to the NWB standard

Language: Python - Size: 6.55 MB - Last synced at: about 1 month ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 0

catalystneuro/dandi-cli Fork of dandi/dandi-cli

DANDI command line client to facilitate common operations

Language: Python - Size: 3.79 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

catalystneuro/pinto-lab-to-nwb

NWB Conversion project for the Pinto lab at the Northwestern University.

Language: Python - Size: 4.36 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1