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    419 repositories

    • deep-neurographs

      Public
      A Python package that corrects split mistakes in a fragmented neuron segmentation using a graph neural network.
      Python
      •
      MIT License
      •0•3•0•0•Updated Mar 12, 2025Mar 12, 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•6•53•5•Updated Mar 11, 2025Mar 11, 2025

    • motion_energy_PCA

      Public
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Mar 11, 2025Mar 11, 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•14•0•Updated Mar 11, 2025Mar 11, 2025

    • aibs-informatics-cdk-lib

      Public
      Library for AWS CDK Constructs related to AIBS Informatics Services
      aibs-informatics
      Python
      •
      Other
      •0•1•0•1•Updated Mar 11, 2025Mar 11, 2025

    • MapMySections

      Public
      GitHub starting page for the MapMySections data challenge
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Mar 11, 2025Mar 11, 2025

    • aibs-informatics-aws-utils

      Public
      Library of generic Python AWS utils used by the AIBS Informatics "Marmot" team
      pythonawsaibs-informatics
      Python
      •
      Other
      •0•1•1•1•Updated Mar 11, 2025Mar 11, 2025

    • axonal_connectomics

      Public
      Repository for tools developed for axonal connectomics
      Jupyter Notebook
      •
      Other
      •1•2•3•1•Updated Mar 11, 2025Mar 11, 2025

    • npc_sessions

      Public
      Tools for accessing and packaging data from behavior and epyhys sessions from the Mindscope Neuropixels team, in the cloud.
      Python
      •1•1•53•0•Updated Mar 11, 2025Mar 11, 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 Mar 11, 2025Mar 11, 2025

    • vis

      Public
      Typescript packages for building big-data visualization tools & components, with examples for a variety of common data types & formats
      visualizationwebglbig-datatoolkit
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•0•5•Updated Mar 11, 2025Mar 11, 2025

    • cell_type_mapper

      Public
      Repository for storing prototype functionality implementations for the BKP
      Python
      •
      Other
      •5•23•3•2•Updated Mar 11, 2025Mar 11, 2025

    • MIES

      Public
      Multichannel Igor Electrophysiology Suite
      electrophysiologyigor-prosupported
      IGOR Pro
      •
      Other
      •9•25•289•13•Updated Mar 11, 2025Mar 11, 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 Mar 11, 2025Mar 11, 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 Mar 11, 2025Mar 11, 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 Mar 10, 2025Mar 10, 2025

    • ACE

      Public
      R Shiny app for comparison of annotations (e.g., cell type assignments)
      R
      •
      Other
      •1•1•10•0•Updated Mar 10, 2025Mar 10, 2025

    • bmtk

      Public
      Brain Modeling Toolkit
      pythonsimulationmodelingneuroscienceneural-networksneuroinformaticsneuron
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •91•286•60•9•Updated Mar 10, 2025Mar 10, 2025

    • video_descriptive_statistics

      Public
      Shell
      •
      Other
      •0•0•0•0•Updated Mar 7, 2025Mar 7, 2025

    • aibs-informatics-aws-lambda

      Public
      AWS Lambda library for AIBS Informatics lambda functions
      aibs-informatics
      Python
      •
      Other
      •0•1•0•0•Updated Mar 7, 2025Mar 7, 2025

    • npc_samstim

      Public
      Tools for processing stim data from Sam's DynamicRoutingTask, compatible with data in the cloud.
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 7, 2025Mar 7, 2025

    • np_notebooks

      Public
      Jupyter Notebook
      •3•0•0•0•Updated Mar 6, 2025Mar 6, 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 Mar 4, 2025Mar 4, 2025

    • biomolvec-data

      Public
      Notebooks and scripts used for the Nautilex Hackathon
      HTML
      •1•0•0•0•Updated Mar 3, 2025Mar 3, 2025

    • biomolvec

      Public
      Notebooks and scripts used for the Nautilex Hackathon
      generative-modelgenesmultimodalfoundation-models
      HTML
      •1•0•0•0•Updated Mar 3, 2025Mar 3, 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 Mar 1, 2025Mar 1, 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 Mar 1, 2025Mar 1, 2025

    • mri_image_label_transfer

      Public
      Python
      •0•0•0•0•Updated Mar 1, 2025Mar 1, 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

    • 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