Allen Institute

bmtk

Brain Modeling Toolkit

openscope_databook

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

MIES

Multichannel Igor Electrophysiology Suite

patchseqtools

QC and cell type assignment for patch-seq transcriptomics data

aisynphys

Analysis tools specific to the aiephys multipatch project.

cell_type_mapper

Repository for storing prototype functionality implementations for the BKP

neuroanalysis

Modular analysis tools for neurophysiology data

jem

Repository containing JEM (JSON Electrophysiology Metadata), a web-form for logging metadata during slice electrophysiology experiments.

aics-fms-file-explorer-app

AICS FMS File Explorer Front End

bmtk-workshop

deep-neurographs

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

transcriptomic_clustering

improved clustering pipeline for transcriptomic data

ACE

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

cplAE_MET

Coupled autoencoder extension for MET analysis.

MinneTaskQueue

collection of scripts for running large scale tasks on Microns Data

np_workflows

npc_sessions

Tools for accessing and packaging data from behavior and epyhys sessions from the Mindscope Neuropixels team, in the cloud.

sourcesep

Bulk-RNA-Snakeline

dynamicrouting-summary

Project summary plots & tables, started for onsite retreat Jan 2024.

ephys-analysis-tools

Code base generating formatted data tables that streamlines data analysis process for ephys production metadata.

Extract_Somatic_Features

A pipeline to extract soma and nucleus features from the segmentation of precomputed EM datasets.

np_codeocean

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

np_notebooks

np_tools

General-purpose tools for common tasks encountered in Mindscope Neuropixels workflows.

npc_lims

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

npc_shields

Tools for Neuropixels probe insertion into SHIELD implants: providing suggested targets, recording actual insertions, storing notes.

openscope_psycode

This repository contains the stimulus behind the PsyCode project

Perisomatic_Based_CellTyping

Repository to accompany the manuscript Perisomatic Ultrastructure Efficiently Classifies Cells in Mouse Cortex.

scrattch.taxonomy

Allen Institute Taxonomy building R package