Allen Institute

bmtk

Brain Modeling Toolkit

openscope_databook

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

abc_atlas_access

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

MIES

Multichannel Igor Electrophysiology Suite

scrattch.bigcat

iterative clustering pipeline of big single cell datasets.

cell_type_mapper

Repository for storing prototype functionality implementations for the BKP

ophys_etl_pipelines

Pipelines and modules for processing optical physiology data

scrattch.mapping

Genearlized mapping scripts for RNA-seq and Patch-seq data

brain_observatory_utilities

A repository for analysis tools for data available from the AllenSDK

aics-fms-file-explorer-app

AICS FMS File Explorer Front End

bmtk-workshop

brain_observatory_qc

deep-neurographs

Neuron reconstruction framework that detects and corrects false splits in a predicted segmentation.

ITCXOP2

mtrain_regimens

Repository to track training stages and regimens for visual behavior

ACE

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

cplAE_MET

Coupled autoencoder extension for MET analysis.

dynamic_routing_analysis

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

openscope_psycode

This repository contains the stimulus behind the PsyCode project

np_config

Config fetching from file or Zookeeper - with local backup - repackaging code from AIBS mpeconfig.

np_notebooks

np_queuey

Tools for submitting and processing jobs through a message queue for Mindscope Neuropixels workflows.

npc_lims

Tools to fetch and update paths, metadata and state for Mindscope Neuropixels sessions, in the cloud.

npc_sync

Repackaging of AllenSDK.SyncDataset with extra functionality, compatible with data in the cloud.

openscope_mousemotion

Moving dot stimuli for the OpenScope MouseMotion project

pigeon

A STOMP client with message definitions via Pydantic

schelp

scrattch.taxonomy

Allen Institute Taxonomy building R package

SHIELD_Dynamic_Gating_Analysis

Code to analyze dynamic gating nwbs with data collected using the SHIELD implant

TEM_comms

Pigeon messages for the next generation TEM imaging system