Projects in Awesome Lists by AllenInstitute

This python module simplifies the development of modules that would like to define and check a particular set of input parameters, but be able to flexibly define those inputs in different ways in different contexts.

Last synced: 19 Jul 2025

https://github.com/alleninstitute/visual_behavior_analysis

Python package for analyzing behavioral data for Brain Observatory: Visual Behavior

behavior neuroscience psychology psychophysics python

Last synced: 11 Apr 2025

https://github.com/alleninstitute/argschema

This python module simplifies the development of modules that would like to define and check a particular set of input parameters, but be able to flexibly define those inputs in different ways in different contexts.

Last synced: 11 Apr 2025

https://alleninstitute.github.io/dipde/

Numerical solver for coupled population density equations

modeling neuroinformatics neuroscience python scientific-computations

Last synced: 05 Apr 2026

https://github.com/alleninstitute/cell_type_mapper

Repository for storing prototype functionality implementations for the BKP

Last synced: 11 Apr 2025

https://github.com/alleninstitute/brain_observatory_examples

Gallery of visualizations and analyses of the Allen Brain Observatory

Last synced: 23 Oct 2025

https://github.com/alleninstitute/swdb_2019

Repository for course materials for the Summer Workshop on the Dynamic Brain 2019

Last synced: 16 Jun 2025

https://github.com/alleninstitute/dipde

Numerical solver for coupled population density equations

modeling neuroinformatics neuroscience python scientific-computations

Last synced: 11 Apr 2025

https://github.com/alleninstitute/tasic2018analysis

Scripts related to VISp and ALM scRNA-seq and FISH analysis for Tasic, et al., 2018.

Last synced: 10 Aug 2025

https://github.com/alleninstitute/mtg_celltypes

Human cortical cell types

Last synced: 08 Oct 2025

https://github.com/alleninstitute/biccn_m1_evo

Analysis for BICCN cross-species primary motor cortex project

Last synced: 11 Apr 2025

https://github.com/alleninstitute/swdb_2018

Course materials for the 2018 Summer Workshop on the Dynamic Brain

Last synced: 11 Apr 2025

https://github.com/alleninstitute/neuron_morphology

Tools for working with single-neuron morphological reconstructions

Last synced: 11 Apr 2025

https://github.com/alleninstitute/micronsbinder

A collection of notebooks to provide examples of using Microns-explorer.org datasets

Last synced: 11 Apr 2025

https://github.com/alleninstitute/mies

Multichannel Igor Electrophysiology Suite

electrophysiology igor-pro supported

Last synced: 07 Jan 2026

https://github.com/alleninstitute/patchseqtools

QC and cell type assignment for patch-seq transcriptomics data

Last synced: 02 Feb 2026

https://github.com/alleninstitute/visual_coding_2p_analysis

Visual Coding 2P analysis code

Last synced: 03 Aug 2025

https://github.com/alleninstitute/mfishtools

Building Gene Sets and Mapping mFISH Data

Last synced: 07 Jan 2026

https://github.com/alleninstitute/all-active-workflow

Creating the code base for All-active Model generation written on top of Bluepyopt

Last synced: 11 Apr 2025

https://github.com/alleninstitute/scrattch.mapping

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

Last synced: 14 Sep 2025

https://github.com/alleninstitute/asap-modules

Shared repo for EM connectomics and Array Tomography render based image processing modules

Last synced: 07 Jul 2025

https://github.com/alleninstitute/biophys_optimize

Optimization of single-cell biophysically detailed models

Last synced: 11 Apr 2025

https://github.com/alleninstitute/aibsopt

Optical projection tomography microscope for isotropic whole-brain imaging

Last synced: 11 Apr 2025

https://github.com/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.

Last synced: 30 Jan 2026

https://github.com/alleninstitute/open_dataset_tools

Tools for accessing open data sets published by the Allen Institute for Brain Sciences

Last synced: 11 Apr 2025

https://github.com/alleninstitute/nomenclature

This repository contains code to generate standardized cell type nomenclature from an R "dendrogram".

Last synced: 16 Apr 2025

https://github.com/alleninstitute/mousebrainhierarchy

Last synced: 11 Apr 2025

https://github.com/alleninstitute/nuccelltypes

Last synced: 07 Jan 2026

https://github.com/alleninstitute/drcme

Dimensionality-reduction and classification for morphology and electrophysiology

Last synced: 11 Apr 2025

https://github.com/alleninstitute/octodac

8 channel analog output shield for Arduino Uno

Last synced: 11 Apr 2025

https://github.com/alleninstitute/allensdk.eye_tracking

Allen Institute mouse eye tracker.

Last synced: 11 Apr 2025

https://github.com/alleninstitute/pytic

PyTic - An Object-Oriented Python Wrapper for Pololu Tic Stepper Drivers

Last synced: 09 Oct 2025

https://github.com/AllenInstitute/MouseBrainHierarchy

Last synced: 01 May 2025

https://github.com/alleninstitute/swdb_2017

course materials for the 2017 Summer Workshop on the Dynamic Brain

Last synced: 07 Jan 2026

https://github.com/alleninstitute/ophys_etl_pipelines

Pipelines and modules for processing optical physiology data

Last synced: 11 Apr 2025

https://github.com/alleninstitute/scrattch.io

Functions for handling RNA-seq files and formats as input and output for scrattch functions.

10xgenomics hdf5 loom r tome transcriptomics

Last synced: 03 Aug 2025

https://github.com/alleninstitute/aifi-swanson-teaseq

Code related to Swanson, et. al. for TEA-seq, ICICLE-seq, and scATAC-seq data processing, analysis, and visualization

atac-seq icicle-seq scatac-seq tea-seq

Last synced: 11 Apr 2025

https://github.com/alleninstitute/mouse_aging_scrnaseq

analysis scripts related to Jin et al manuscript on scRNA seq in aging mouse brain

Last synced: 08 Apr 2025

https://github.com/alleninstitute/tasic2016data

Single cell transcriptomic data from Tasic, et al. (2016)

scrattch scrna-seq-data transcriptomics

Last synced: 11 Apr 2025

https://github.com/AllenInstitute/GeneOrthology

CSV file and R package for collecting gene ortholog information from NCBI.

Last synced: 02 May 2025

https://github.com/alleninstitute/all-active-manuscript

Code for reproducing the figures presented in: Single-neuron models linking electrophysiology, morphology and transcriptomics across cortical cell types

Last synced: 11 Jun 2025

https://github.com/alleninstitute/coupledae-patchseq

Multimodal data alignment and cell type analysis with coupled autoencoders.

autoencoders celltypes multimodal patchseq representation-learning

Last synced: 11 Apr 2025

https://github.com/alleninstitute/zeromq-xop

The ZeroMQ XOP enables Igor Pro to interface over the network using a ZeroMQ messaging layer and JSON as message format

Last synced: 07 Sep 2025

https://github.com/alleninstitute/geneorthology

CSV file and R package for collecting gene ortholog information from NCBI.

Last synced: 11 Apr 2025

https://github.com/alleninstitute/stpt_registration

STPT registration methods

Last synced: 29 Oct 2025

https://github.com/alleninstitute/sea-ad_2024

Last synced: 11 Apr 2025

https://github.com/alleninstitute/neuroanalysis

Modular analysis tools for neurophysiology data

Last synced: 11 Apr 2025

https://github.com/alleninstitute/swdb_2017_tools

A collaborative Python package built by participants of the Summer Workshop on the Dynamic Brain

Last synced: 30 Aug 2025

https://github.com/alleninstitute/glif_teeter_et_al_2018

Analysis code for Teeter et al 2018 Nature Communications Manuscript

Last synced: 04 Mar 2026

https://github.com/alleninstitute/aics-automated-cell-culture-workflow

Venus method files in the “.pkg” format for the Semi Automated Passaging, Seeding and Maintenance, of the Allen cell collection of hiPSC lines expressing green fluorescent protein tagged to protein identifying specific cellular organelles and structures.

Last synced: 07 Jan 2026

https://github.com/alleninstitute/piteam

Parallel Imaging Pipeline Using Transmission Electron Automated Microscopes (piTEAM)

Last synced: 28 Jan 2026

https://github.com/alleninstitute/ofs-em-connectomics

Code and data for the 2021 Open for Science tutorial for EM connectomics.

Last synced: 04 Oct 2025

https://github.com/alleninstitute/nwb-api

Last synced: 23 Feb 2026

https://github.com/alleninstitute/render-python

A python interface for render

Last synced: 11 Apr 2025

https://github.com/alleninstitute/3d-atlas-reverse-mapping

This repository contains a Jupyter Notebook that demonstrates the reverse mapping of the 3D atlas onto an imaged section.

Last synced: 11 Apr 2025

https://github.com/alleninstitute/ccfv3_volumetric_analysis

Scripts for measuring surface area and volumes of structures in both the reference and original spaces.

Last synced: 11 Apr 2025

https://github.com/alleninstitute/u-dagan

Unsupervised data augmentation using GANs.

Last synced: 30 Jul 2025

https://github.com/alleninstitute/ccf_tutorial

Last synced: 11 Apr 2025

https://github.com/alleninstitute/spatial_compare

package for comparing spatial transcriptomics datasets

Last synced: 10 Aug 2025

https://github.com/alleninstitute/merquaco

Last synced: 11 Apr 2025

https://github.com/alleninstitute/l5_ven

This repository contains code for reproducing the analysis of snRNA-seq data from human fronto-insula

Last synced: 11 Apr 2025

https://github.com/alleninstitute/neuropixels_platform_paper

Code used to generate figures for Siegle, Jia et al. (2019)

Last synced: 16 Mar 2026

https://github.com/alleninstitute/swdb_2021

Last synced: 11 Apr 2025

https://github.com/alleninstitute/coupledae

Repository for NeurIPS 2019 paper

Last synced: 11 Apr 2025

https://github.com/alleninstitute/enhancerbenchmark

Last synced: 11 Mar 2026

https://github.com/alleninstitute/arkhipov2018_layer4

Modeling code related to Arkhipov 2018 publication

Last synced: 29 Oct 2025

https://github.com/alleninstitute/patchseq_human_l23

Code for reproducing the analyses presented in "Human cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neurons".

Last synced: 07 Jan 2026

https://github.com/alleninstitute/human_cross_areal

Human cellular diversity across cortex

Last synced: 11 Apr 2025

https://github.com/alleninstitute/vis

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

big-data toolkit visualization webgl

Last synced: 11 Apr 2025