Pinned Repositories
abc_atlas_access
Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas
AllenSDK
code for reading and processing Allen Institute for Brain Science data
bmtk
Brain Modeling Toolkit
deepinterpolation
dipde
Numerical solver for coupled population density equations
ecephys_spike_sorting
Modules for processing extracellular electrophysiology data from Neuropixels probes
openai_tools
Growing collection of scripts to summarize the scientific literature using large-language models like ChatGPT.
openscope_databook
OpenScope databook: a collaborative, versioned, data-centric collection of foundational analyses for reproducible systems neuroscience 🐁🧠🔬🖥️📈
scrattch.hicat
Hierarchical, iterative clustering for analysis of transcriptomics data in R
sonata
Collaboration between BBP and AIBS
AllenInstitute's Repositories
AllenInstitute/bmtk
Brain Modeling Toolkit
AllenInstitute/openscope_databook
OpenScope databook: a collaborative, versioned, data-centric collection of foundational analyses for reproducible systems neuroscience 🐁🧠🔬🖥️📈
AllenInstitute/abc_atlas_access
Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas
AllenInstitute/MIES
Multichannel Igor Electrophysiology Suite
AllenInstitute/cell_type_mapper
Repository for storing prototype functionality implementations for the BKP
AllenInstitute/ZeroMQ-XOP
The ZeroMQ XOP enables Igor Pro to interface over the network using a ZeroMQ messaging layer and JSON as message format
AllenInstitute/biofile-finder
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.
AllenInstitute/vis
Typescript packages for building big-data visualization tools & components, with examples for a variety of common data types & formats
AllenInstitute/deep-neurographs
A Python package that corrects split mistakes in a fragmented neuron segmentation using a graph neural network.
AllenInstitute/jem
Repository containing JEM (JSON Electrophysiology Metadata), a web-form for logging metadata during slice electrophysiology experiments.
AllenInstitute/mtrain_regimens
Repository to track training stages and regimens for visual behavior
AllenInstitute/axonal_connectomics
Repository for tools developed for axonal connectomics
AllenInstitute/AllenInstituteTaxonomy
AllenInstitute/cplAE_MET
Coupled autoencoder extension for MET analysis.
AllenInstitute/dynamic_routing_analysis
Tools for accessing, processing and presenting data from Dynamic Routing experiments.
AllenInstitute/motion_energy_PCA
AllenInstitute/sciduck
AllenInstitute/scrattch.taxonomy
Allen Institute Taxonomy building R package
AllenInstitute/MicronsFunctionalConnectomics
Code for "Functional connectomics spanning multiple areas of mouse visual cortex" by MICrONs Consortium et al.
AllenInstitute/cell_type_constellations
Prototype utilities for creating constellation plots based on cell type taxonomies.
AllenInstitute/compute_motion_energy
Step 2 of Behavior Video QC pipeline. Loads video Barr files and computes motion energy in 3d and
AllenInstitute/DemoMkdocsOpenAPI
Repository to be nested in DemoDocumentation
AllenInstitute/load_behavior_video
First step in behavior video QC pipeline. Loads attached videos, saves gray frames in zarr file, saves metadata.
AllenInstitute/neuroglancer
WebGL-based viewer for volumetric data
AllenInstitute/npc_lims
Tools to fetch and update paths, metadata and state for Mindscope Neuropixels sessions, in the cloud.
AllenInstitute/npc_sessions_cache
Scripts, notebooks and plots that operate on NWB or NWB-like objects from `npc_sessions` in the cloud.
AllenInstitute/npc_sync
Repackaging of AllenSDK.SyncDataset with extra functionality, compatible with data in the cloud.
AllenInstitute/openscope_mousemotion
Moving dot stimuli for the OpenScope MouseMotion project
AllenInstitute/pigeon
A STOMP client with message definitions via Pydantic
AllenInstitute/TEM_config