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    415 repositories

    • MIES

      Public
      Multichannel Igor Electrophysiology Suite
      electrophysiologyigor-prosupported
      IGOR Pro
      •
      Other
      •9•25•288•9•Updated Feb 28, 2025Feb 28, 2025

    • npc_ephys

      Public
      Tools for accessing and processing raw ephys data, compatible with data in the cloud.
      Python
      •
      MIT License
      •2•0•0•0•Updated Feb 28, 2025Feb 28, 2025

    • motion_energy_PCA

      Public
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Feb 28, 2025Feb 28, 2025

    • compute_motion_energy

      Public
      Step 2 of Behavior Video QC pipeline. Loads video Barr files and computes motion energy in 3d and
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Feb 28, 2025Feb 28, 2025

    • bmtk

      Public
      Brain Modeling Toolkit
      pythonsimulationmodelingneuroscienceneural-networksneuroinformaticsneuron
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •91•284•60•10•Updated Feb 27, 2025Feb 27, 2025

    • cell_type_constellations

      Public
      Prototype utilities for creating constellation plots based on cell type taxonomies.
      Python
      •2•0•0•0•Updated Feb 27, 2025Feb 27, 2025

    • video_descriptive_statistics

      Public
      Shell
      •
      Other
      •0•0•0•0•Updated Feb 27, 2025Feb 27, 2025

    • dynamic_routing_analysis

      Public
      Tools for accessing, processing and presenting data from Dynamic Routing experiments.
      Jupyter Notebook
      •0•1•0•0•Updated Feb 27, 2025Feb 27, 2025

    • biofile-finder

      Public
      An open-use web application created for easy access, collaboration, and sharing of datasets through rich metadata search, filter, sort, and direct viewing in common industry applications or in our web-based 3D Volume Viewer.
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •2•5•51•5•Updated Feb 27, 2025Feb 27, 2025

    • deep-neurographs

      Public
      A Python package that utilizes machine learning to correct split mistakes in a fragmented neuron segmentation.
      Python
      •
      MIT License
      •0•3•0•0•Updated Feb 27, 2025Feb 27, 2025

    • load_behavior_video

      Public
      First step in behavior video QC pipeline. Loads attached videos, saves gray frames in zarr file, saves metadata.
      Jupyter Notebook
      •0•0•0•0•Updated Feb 27, 2025Feb 27, 2025

    • jem

      Public
      Repository containing JEM (JSON Electrophysiology Metadata), a web-form for logging metadata during slice electrophysiology experiments.
      HTML
      •
      Other
      •3•3•0•0•Updated Feb 27, 2025Feb 27, 2025

    • npc_lims

      Public
      Tools to fetch and update paths, metadata and state for Mindscope Neuropixels sessions, in the cloud.
      Python
      •
      MIT License
      •0•0•3•0•Updated Feb 27, 2025Feb 27, 2025

    • cell_type_mapper

      Public
      Repository for storing prototype functionality implementations for the BKP
      Python
      •
      Other
      •5•23•5•2•Updated Feb 27, 2025Feb 27, 2025

    • scrattch

      Public
      Single cell RNA-seq analysis for transcriptomic type characterization
      rumbrellatranscriptomicsscrattch
      R
      •
      Other
      •3•36•0•0•Updated Feb 26, 2025Feb 26, 2025

    • behavior_video_qc_visualization

      Public
      Part of behavior video qc pipeline. Collects results from descriptive statistics, motion energy, and PCA capsules to plot them for qc visualization
      0•0•0•0•Updated Feb 26, 2025Feb 26, 2025

    • scrattch.taxonomy

      Public
      Allen Institute Taxonomy building R package
      HTML
      •1•1•9•0•Updated Feb 26, 2025Feb 26, 2025

    • mtrain_regimens

      Public
      Repository to track training stages and regimens for visual behavior
      Python
      •
      Other
      •4•3•14•0•Updated Feb 25, 2025Feb 25, 2025

    • openscope_mousemotion

      Public
      Moving dot stimuli for the OpenScope MouseMotion project
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Feb 25, 2025Feb 25, 2025

    • AllenInstituteTaxonomy

      Public
      0•2•4•0•Updated Feb 24, 2025Feb 24, 2025

    • axonal_connectomics

      Public
      Repository for tools developed for axonal connectomics
      Jupyter Notebook
      •
      Other
      •1•2•3•1•Updated Feb 24, 2025Feb 24, 2025

    • ZeroMQ-XOP

      Public
      The ZeroMQ XOP enables Igor Pro to interface over the network using a ZeroMQ messaging layer and JSON as message format
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •8•9•9•0•Updated Feb 24, 2025Feb 24, 2025

    • MicronsFunctionalConnectomics

      Public
      Code for "Functional connectomics spanning multiple areas of mouse visual cortex" by MICrONs Consortium et al.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Feb 23, 2025Feb 23, 2025

    • abc_atlas_access

      Public
      Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas
      Jupyter Notebook
      •
      Other
      •24•59•13•6•Updated Feb 21, 2025Feb 21, 2025

    • openscope_databook

      Public
      OpenScope databook: a collaborative, versioned, data-centric collection of foundational analyses for reproducible systems neuroscience 🐁🧠🔬🖥️📈
      visualizationpythonreproducible-researchdata-visualizationdata-analysisnwbdandi-archive
      Python
      •
      Other
      •21•64•13•4•Updated Feb 21, 2025Feb 21, 2025

    • sciduck

      Public
      Jupyter Notebook
      •4•1•5•0•Updated Feb 21, 2025Feb 21, 2025

    • neuroglancer

      Public
      WebGL-based viewer for volumetric data
      TypeScript
      •
      Apache License 2.0
      •311•0•0•0•Updated Feb 21, 2025Feb 21, 2025

    • TEM_config

      Public
      1•0•1•1•Updated Feb 21, 2025Feb 21, 2025

    • npc_sessions_cache

      Public
      Scripts, notebooks and plots that operate on NWB or NWB-like objects from `npc_sessions` in the cloud.
      Jupyter Notebook
      •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

    • pigeon

      Public
      A STOMP client with message definitions via Pydantic
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•0•Updated Feb 19, 2025Feb 19, 2025