Repositories list

• 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 8, 2025Mar 8, 2025

• MIES

  Public
  Multichannel Igor Electrophysiology Suite

  electrophysiologyigor-prosupported

  IGOR Pro

  •

  Other

  •9•25•288•12•Updated Mar 8, 2025Mar 8, 2025

• axonal_connectomics

  Public
  Repository for tools developed for axonal connectomics

  Jupyter Notebook

  •

  Other

  •1•2•3•1•Updated Mar 8, 2025Mar 8, 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•6•Updated Mar 7, 2025Mar 7, 2025

• video_descriptive_statistics

  Public
  Shell

  •

  Other

  •0•0•0•0•Updated Mar 7, 2025Mar 7, 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 7, 2025Mar 7, 2025

• motion_energy_PCA

  Public
  Jupyter Notebook

  •

  Other

  •0•1•0•0•Updated Mar 7, 2025Mar 7, 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 7, 2025Mar 7, 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 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

• bmtk

  Public
  Brain Modeling Toolkit

  pythonsimulationmodeling+ 4neuroscienceneural-networksneuroinformaticsneuron

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •91•286•60•9•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

• 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 7, 2025Mar 7, 2025

• np_notebooks

  Public
  Jupyter Notebook

  •3•0•0•0•Updated Mar 6, 2025Mar 6, 2025

• vis

  Public
  Typescript packages for building big-data visualization tools & components, with examples for a variety of common data types & formats

  visualizationwebglbig-data+ 1toolkit

  TypeScript

  •

  BSD 3-Clause "New" or "Revised" License

  •0•5•0•6•Updated Mar 5, 2025Mar 5, 2025

• ACE

  Public
  R Shiny app for comparison of annotations (e.g., cell type assignments)

  R

  •

  Other

  •1•1•10•0•Updated Mar 4, 2025Mar 4, 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

• cell_type_mapper

  Public
  Repository for storing prototype functionality implementations for the BKP

  Python

  •

  Other

  •5•23•3•2•Updated Mar 4, 2025Mar 4, 2025

• openscope_databook

  Public
  OpenScope databook: a collaborative, versioned, data-centric collection of foundational analyses for reproducible systems neuroscience 🐁🧠🔬🖥️📈

  visualizationpythonreproducible-research+ 4data-visualizationdata-analysisnwbdandi-archive

  Python

  •

  Other

  •21•64•13•4•Updated Mar 3, 2025Mar 3, 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-modelgenesmultimodal+ 1foundation-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

• 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

• 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

• scrattch

  Public
  Single cell RNA-seq analysis for transcriptomic type characterization

  rumbrellatranscriptomics+ 1scrattch

  R

  •

  Other

  •3•36•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