Discover AllenInstitute/All-active-Workflow Open Source project

Growing collection of scripts to summarize the scientific literature using large-language models like ChatGPT.

340

bmtk

Brain Modeling Toolkit

deepinterpolation

openai_tools

Hierarchical, iterative clustering for analysis of transcriptomics data in R

109

scrattch.hicat

Modules for processing extracellular electrophysiology data from Neuropixels probes

105

ecephys_spike_sorting

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

105

openscope_databook

Collaboration between BBP and AIBS

sonata

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

abc_atlas_access

AICS Segmentation (One-Way) Mirror

aics-segmentation

Python package providing mesoscale connectivity models for mouse.

mouse_connectivity_models

a Python machine learning library for neurophysiology data

neuroglia

COmmon COordinate FRAMEwork in R

cocoframer

MicronsBinder

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

Single cell RNA-seq analysis for transcriptomic type characterization

scrattch

aics-ml-segmentation

AICS ML Segmentation (One-Way) Mirror

computes intrinsic cell features from intracellular electrophysiology data

ipfx

Gallery of visualizations and analyses of the Allen Brain Observatory

brain_observatory_examples

scRNA-seq data visualization from scrattch

tasic2018analysis

scrattch.vis

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.

Human cortical cell types

MTG_celltypes

SWDB_2019

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

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

visual_behavior_analysis

Multichannel Igor Electrophysiology Suite

MIES

IGOR Pro

BICCN_M1_Evo

Analysis for BICCN cross-species primary motor cortex project

Course materials for the 2018 Summer Workshop on the Dynamic Brain

SWDB_2018

Repository to host materials for the summer workshop on the dynamic brain

swdb_2022

Numerical solver for coupled population density equations

dipde

Tools for working with single-neuron morphological reconstructions

neuron_morphology

Repository for storing prototype functionality implementations for the BKP

cell_type_mapper

Optical projection tomography microscope for isotropic whole-brain imaging

AIBSOPT

QC and cell type assignment for patch-seq transcriptomics data

patchseqtools

Optimization of single-cell biophysically detailed models

biophys_optimize

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

asap-modules

Visual Coding 2P analysis code

visual_coding_2p_analysis

NucCellTypes

Dimensionality-reduction and classification for morphology and electrophysiology

drcme

MouseBrainHierarchy

Allen Institute mouse eye tracker.

allensdk.eye_tracking

8 channel analog output shield for Arduino Uno

octoDAC

C++

nomenclature

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

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

scrattch.io

mfishtools

Building Gene Sets and Mapping mFISH Data

course materials for the 2017 Summer Workshop on the Dynamic Brain

SWDB_2017

Pipelines and modules for processing optical physiology data

aifi-swanson-teaseq

ophys_etl_pipelines

iterative clustering pipeline of big single cell datasets.

scrattch.bigcat

tasic2016data

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

ZeroMQ-XOP

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

nwb-api

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

open_dataset_tools

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

pytic

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

All-active-Manuscript

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

swdb_2017_tools

Publication-ready visualization of overlays of imagery and segmentation from cloudvolume data

ImageryClient

Multimodal data alignment and cell type analysis with coupled autoencoders.

coupledAE-patchseq

Parallel Imaging Pipeline Using Transmission Electron Automated Microscopes (piTEAM)

piTEAM

scrattch.mapping

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

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.

pcg_skel

Robust skeletonization of PyChunkedGraph-backed objects

A python interface for render

render-python

Analysis code for Teeter et al 2018 Nature Communications Manuscript

GLIF_Teeter_et_al_2018

Repository for NeurIPS 2019 paper

coupledAE

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

neuropixels_platform_paper

Unsupervised data augmentation using GANs.

U-DAGAN

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

3D-atlas-reverse-mapping

A repository for student code for the 2019 Summer Workshop on the Dynamic Brain

swdb_2019_student

Modeling code related to Arkhipov 2018 publication

arkhipov2018_layer4

STPT registration methods

stpt_registration

C++

CCF_Tutorial

swdb_2021

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

patchseq_human_L23

An simplified interface for making dash apps to explore multi-dimensional dataframes with custom link integration and filtering.

DashDataFrame

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

L5_VEN

CCFv3_Volumetric_Analysis

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

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

OFS-EM-Connectomics

Human cellular diversity across cortex

human_cross_areal

Resources for Allen Instutite tutorials presented at CNS 2021

CNS_2021

deepinterpolation_nextflow

align a 3D data set to another

em_coregistration

Classifying regions of interest in mouse brain as cell or not cell

croissant

Creates the pink noise stimuli used in the noise1, noise2, and ramp to rheo stimulus used in the Allen Institute for Brain Science electrophysiology pipeline.

ephys_pink_noise

EM microscopy lens correction

em_stitch

Notebooks and design files for Allen Brain Observatory experimental procedures

neuropixels_protocol_resources

bmtk-workshop

snRNA-seq of temporal cortex in great apes

Great_Ape_MTG

A repository for analysis tools for data available from the AllenSDK

brain_observatory_utilities

tools for plotting swc and meshparty skeletons

skeleton_plot

deepinterpolation_paper

Guidebook

GLIFS plus after spike currents

GLIFS_ASC

supporting data and code for human L1 patchSeq manuscript

patchseq_human_L1

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

jem

ophys_nway_matching

Code and scripts for used in the generation of cortical streamlines and coordinates for the Allen CCF

cortical_coordinates

C++

Contrast_Analysis

Big FeaTure Aligner: a scalable solution for feature alignment

BigFeta

Repository for Smith et al. 2019

PeptidergicNetworks

100

bonsai_workflows

A collection of bonsai workflows developed at the Allen Institute