Repositories list

• MIES

  Public
  Multichannel Igor Electrophysiology Suite

  electrophysiologyigor-prosupported

  IGOR Pro

  •

  Other

  •9•25•286•9•Updated Dec 15, 2024Dec 15, 2024

• txtox

  Public
  Experiments to relate gene expression and anatomical location

  Jupyter Notebook

  •0•0•0•0•Updated Dec 14, 2024Dec 14, 2024

• spatial_compare

  Public
  package for comparing spatial transcriptomics datasets

  Jupyter Notebook

  •

  Other

  •9•4•10•8•Updated Dec 14, 2024Dec 14, 2024

• EM_MC_paper_figures

  Public
  Notebooks for analyzing and generating figures for EM MC paper

  Jupyter Notebook

  •

  Other

  •0•1•0•0•Updated Dec 14, 2024Dec 14, 2024

• ACE

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

  R

  •

  Other

  •1•1•5•0•Updated Dec 14, 2024Dec 14, 2024

• cell_type_mapper

  Public
  Repository for storing prototype functionality implementations for the BKP

  Python

  •

  Other

  •4•18•4•2•Updated Dec 13, 2024Dec 13, 2024

• abc_atlas_access

  Public
  Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas

  Jupyter Notebook

  •

  Other

  •22•54•13•5•Updated Dec 13, 2024Dec 13, 2024

• dynamic_routing_analysis

  Public
  Tools for accessing, processing and presenting data from Dynamic Routing experiments.

  Jupyter Notebook

  •0•1•0•0•Updated Dec 13, 2024Dec 13, 2024

• 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•51•4•Updated Dec 13, 2024Dec 13, 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 Dec 12, 2024Dec 12, 2024

• cplAE_MET

  Public
  Coupled autoencoder extension for MET analysis.

  Jupyter Notebook

  •0•1•0•0•Updated Dec 12, 2024Dec 12, 2024

• 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 Dec 12, 2024Dec 12, 2024

• np_codeocean

  Public
  Tools for uploading and interacting with Mindscope Neuropixels experiments on Code Ocean

  Python

  •2•0•1•1•Updated Dec 12, 2024Dec 12, 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 Dec 12, 2024Dec 12, 2024

• sciduck

  Public
  Jupyter Notebook

  •2•1•4•0•Updated Dec 12, 2024Dec 12, 2024

• TEM_config

  Public
  0•0•1•0•Updated Dec 11, 2024Dec 11, 2024

• motion_energy_PCA

  Public
  Python

  •

  Other

  •0•0•0•0•Updated Dec 10, 2024Dec 10, 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 Dec 10, 2024Dec 10, 2024

• axonal_connectomics

  Public
  Repository for tools developed for axonal connectomics

  Jupyter Notebook

  •

  Other

  •1•2•3•0•Updated Dec 9, 2024Dec 9, 2024

• np_notebooks

  Public
  Jupyter Notebook

  •3•0•0•0•Updated Dec 7, 2024Dec 7, 2024

• HMBA_BasalGanglia_Consensus_Taxonomy

  Public
  SCSS

  •

  Creative Commons Zero v1.0 Universal

  •0•0•0•0•Updated Dec 7, 2024Dec 7, 2024

• 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•54•0•Updated Dec 6, 2024Dec 6, 2024

• npc_stim

  Public
  Tools for accessing and processing stim data, compatible with data in the cloud.

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 6, 2024Dec 6, 2024

• BigFeta

  Public
  Big FeaTure Aligner: a scalable solution for feature alignment

  Python

  •

  BSD 2-Clause "Simplified" License

  •2•3•4•0•Updated Dec 6, 2024Dec 6, 2024

• 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

  •20•64•13•0•Updated Dec 5, 2024Dec 5, 2024

• vis

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

  TypeScript

  •

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

  •0•5•0•2•Updated Dec 4, 2024Dec 4, 2024

• 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 Dec 4, 2024Dec 4, 2024

• npc_session

  Public
  Basic tools for parsing subject, session, date and time associated with data from the Mindscope Neuropixels team, in the cloud.

  Python

  •0•0•0•0•Updated Dec 4, 2024Dec 4, 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•13•1•Updated Dec 4, 2024Dec 4, 2024

• 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 Dec 4, 2024Dec 4, 2024