Skip to content

@AllenInstitute Allen Institute

Change the repository type filter

All

    Repositories list

    410 repositories

    • scrattch.mapping

      Public
      Genearlized mapping scripts for RNA-seq and Patch-seq data
      R
      •2•11•8•0•Updated Jan 27, 2025Jan 27, 2025

    • txtox

      Public
      Experiments to relate gene expression and anatomical location
      Jupyter Notebook
      •0•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • TEM_comms

      Public
      Pigeon messages for the next generation TEM imaging system
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•1•0•Updated Jan 27, 2025Jan 27, 2025

    • MIES

      Public
      Multichannel Igor Electrophysiology Suite
      electrophysiologyigor-prosupported
      IGOR Pro
      •
      Other
      •9•25•292•8•Updated Jan 27, 2025Jan 27, 2025

    • AllenInstituteTaxonomy

      Public
      0•1•4•0•Updated Jan 27, 2025Jan 27, 2025

    • mtrain_regimens

      Public
      Repository to track training stages and regimens for visual behavior
      Python
      •
      Other
      •4•3•14•0•Updated Jan 27, 2025Jan 27, 2025

    • scrattch.taxonomy

      Public
      Allen Institute Taxonomy building R package
      HTML
      •1•1•10•0•Updated Jan 27, 2025Jan 27, 2025

    • bmtk

      Public
      Brain Modeling Toolkit
      pythonsimulationmodelingneuroscienceneural-networksneuroinformaticsneuron
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •89•281•58•10•Updated Jan 27, 2025Jan 27, 2025

    • abc_atlas_access

      Public
      Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas
      Jupyter Notebook
      •
      Other
      •23•58•14•4•Updated Jan 27, 2025Jan 27, 2025

    • cell_type_mapper

      Public
      Repository for storing prototype functionality implementations for the BKP
      Python
      •
      Other
      •4•21•5•2•Updated Jan 27, 2025Jan 27, 2025

    • openscope_mousemotion

      Public
      Moving dot stimuli for the OpenScope MouseMotion project
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • deep-neurographs

      Public
      A Python package that utilizes machine learning to correct split mistakes in a fragmented neuron segmentation.
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Jan 25, 2025Jan 25, 2025

    • cplAE_MET

      Public
      Coupled autoencoder extension for MET analysis.
      Jupyter Notebook
      •0•1•0•0•Updated Jan 24, 2025Jan 24, 2025

    • spatial_compare

      Public
      package for comparing spatial transcriptomics datasets
      Jupyter Notebook
      •
      Other
      •9•5•10•6•Updated Jan 24, 2025Jan 24, 2025

    • scrattch.patchseq

      Public
      R
      •1•0•0•1•Updated Jan 24, 2025Jan 24, 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 Jan 23, 2025Jan 23, 2025

    • np_pipeline_qc

      Public
      Python
      •3•0•4•0•Updated Jan 23, 2025Jan 23, 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 Jan 23, 2025Jan 23, 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 Jan 23, 2025Jan 23, 2025

    • dynamic_routing_analysis

      Public
      Tools for accessing, processing and presenting data from Dynamic Routing experiments.
      Jupyter Notebook
      •0•1•0•0•Updated Jan 22, 2025Jan 22, 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
      •1•4•60•4•Updated Jan 21, 2025Jan 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 Jan 21, 2025Jan 21, 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 Jan 18, 2025Jan 18, 2025

    • sciduck

      Public
      Jupyter Notebook
      •3•1•4•0•Updated Jan 18, 2025Jan 18, 2025

    • axonal_connectomics

      Public
      Repository for tools developed for axonal connectomics
      Jupyter Notebook
      •
      Other
      •1•2•3•0•Updated Jan 18, 2025Jan 18, 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
      •20•64•13•2•Updated Jan 17, 2025Jan 17, 2025

    • scrattch

      Public
      Single cell RNA-seq analysis for transcriptomic type characterization
      rumbrellatranscriptomicsscrattch
      R
      •
      Other
      •3•35•0•0•Updated Jan 17, 2025Jan 17, 2025

    • pertpy

      Public
      Perturbation Analysis in the scverse ecosystem.
      Python
      •
      MIT License
      •25•0•0•0•Updated Jan 16, 2025Jan 16, 2025

    • licking_behavior_NP

      Public
      Analysis of mouse licking behavior during visually guided behavior
      Python
      •1•0•1•0•Updated Jan 16, 2025Jan 16, 2025

    • merquaco-pc-test

      Public
      Jupyter Notebook
      •
      Other
      •3•0•0•0•Updated Jan 16, 2025Jan 16, 2025