Skip to content

@AllenInstitute Allen Institute

Change the repository type filter

All

    Repositories list

    397 repositories

    • 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•3•40•5•Updated Nov 13, 2024Nov 13, 2024

    • cell_type_mapper

      Public
      Repository for storing prototype functionality implementations for the BKP
      Python
      •
      Other
      •4•18•4•2•Updated Nov 13, 2024Nov 13, 2024

    • 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
      •19•63•11•2•Updated Nov 13, 2024Nov 13, 2024

    • txtox

      Public
      Experiments to relate gene expression and anatomical location
      Jupyter Notebook
      •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

    • scrattch.mapping

      Public
      Genearlized mapping scripts for RNA-seq and Patch-seq data
      R
      •2•10•8•0•Updated Nov 13, 2024Nov 13, 2024

    • scrattch.taxonomy

      Public
      Allen Institute Taxonomy building R package
      HTML
      •1•1•7•1•Updated Nov 13, 2024Nov 13, 2024

    • abc_atlas_access

      Public
      Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas
      Jupyter Notebook
      •
      Other
      •21•50•12•5•Updated Nov 13, 2024Nov 13, 2024

    • axonal_connectomics

      Public
      Repository for tools developed for axonal connectomics
      Jupyter Notebook
      •
      Other
      •1•2•3•0•Updated Nov 13, 2024Nov 13, 2024

    • deep-neurographs

      Public
      Deep-Neurographs is a Python module that utilizes machine learning to detect and correct false splits in a predicted neuron segmentation.
      Python
      •
      MIT License
      •0•3•0•0•Updated Nov 13, 2024Nov 13, 2024

    • asap-modules

      Public
      Shared repo for EM connectomics and Array Tomography render based image processing modules
      Python
      •
      BSD 2-Clause "Simplified" License
      •4•14•12•2•Updated Nov 12, 2024Nov 12, 2024

    • EM_MC_paper_figures

      Public
      Notebooks for analyzing and generating figures for EM MC paper
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Nov 12, 2024Nov 12, 2024

    • dynamic_routing_analysis

      Public
      Tools for accessing, processing and presenting data from Dynamic Routing experiments.
      Jupyter Notebook
      •0•1•0•0•Updated Nov 12, 2024Nov 12, 2024

    • bmtk

      Public
      Brain Modeling Toolkit
      pythonsimulationmodelingneuroscienceneural-networksneuroinformaticsneuron
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •88•273•58•8•Updated Nov 12, 2024Nov 12, 2024

    • np_notebooks

      Public
      Jupyter Notebook
      •3•0•0•0•Updated Nov 12, 2024Nov 12, 2024

    • mtrain_regimens

      Public
      Repository to track training stages and regimens for visual behavior
      Python
      •
      Other
      •4•2•14•0•Updated Nov 12, 2024Nov 12, 2024

    • scrattch.bigcat

      Public
      iterative clustering pipeline of big single cell datasets.
      R
      •10•26•4•2•Updated Nov 11, 2024Nov 11, 2024

    • merquaco

      Public
      Jupyter Notebook
      •
      Other
      •2•1•0•0•Updated Nov 11, 2024Nov 11, 2024

    • compute_motion_energy

      Public
      Step 2 of Behavior Video QC pipeline. Loads video Barr files and computes motion energy in 3d and
      Shell
      •
      Other
      •0•0•0•0•Updated Nov 11, 2024Nov 11, 2024

    • pigeon

      Public
      A STOMP client with message definitions via Pydantic
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•0•Updated Nov 9, 2024Nov 9, 2024

    • npc_mvr

      Public
      Tools for reading raw video data from MindScope Neuropixels experiments, compatible with data in the cloud.
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

    • acq4

      Public
      Data acquisition for patch clamp ephys / optogenetics / imaging experiments
      Python
      •
      MIT License
      •49•0•0•0•Updated Nov 7, 2024Nov 7, 2024

    • TEM_comms

      Public
      Pigeon messages for the next generation TEM imaging system
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•0•Updated Nov 7, 2024Nov 7, 2024

    • TEM_config

      Public
      0•0•1•0•Updated Nov 7, 2024Nov 7, 2024

    • 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 Nov 6, 2024Nov 6, 2024

    • coupledAE-patchseq

      Public
      Multimodal data alignment and cell type analysis with coupled autoencoders.
      representation-learningmultimodalcelltypespatchseqautoencoders
      Jupyter Notebook
      •
      Other
      •1•8•2•0•Updated Nov 5, 2024Nov 5, 2024

    • MIES

      Public
      Multichannel Igor Electrophysiology Suite
      electrophysiologyigor-prosupported
      IGOR Pro
      •
      Other
      •7•23•288•11•Updated Nov 5, 2024Nov 5, 2024

    • motion_energy_PCA

      Public
      Shell
      •
      Other
      •0•0•0•0•Updated Nov 4, 2024Nov 4, 2024

    • video_descriptive_statistics

      Public
      Shell
      •
      Other
      •0•0•0•0•Updated Nov 4, 2024Nov 4, 2024

    • np_codeocean

      Public
      Tools for uploading and interacting with Mindscope Neuropixels experiments on Code Ocean
      Python
      •2•0•1•0•Updated Nov 4, 2024Nov 4, 2024

    • 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 Nov 4, 2024Nov 4, 2024