AllenInstitute/AllenSDK

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AllenInstitute/AllenSDK

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code for reading and processing Allen Institute for Brain Science data

The Allen SDK

This repository contains code for processing and analyzing data in the Allen Brain Atlas.

Please visit http://alleninstitute.github.io/AllenSDK for more information.

We welcome contributions! See the contribution guide here. See here for the list of authors.

If you have more general questions or comments about the AllenSDK please post them to the Allen Brain Map Community Forum.

bmtk

Brain Modeling Toolkit

deepinterpolation

openai_tools

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

scrattch.hicat

Hierarchical, iterative clustering for analysis of transcriptomics data in R

ecephys_spike_sorting

Modules for processing extracellular electrophysiology data from Neuropixels probes

openscope_databook

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

sonata

Collaboration between BBP and AIBS

abc_atlas_access

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

Jupyter Notebook

aics-segmentation

AICS Segmentation (One-Way) Mirror

Jupyter Notebook

mouse_connectivity_models

Python package providing mesoscale connectivity models for mouse.

neuroglia

a Python machine learning library for neurophysiology data

cocoframer

COmmon COordinate FRAMEwork in R

MicronsBinder

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

Jupyter Notebook

scrattch

Single cell RNA-seq analysis for transcriptomic type characterization

aics-ml-segmentation

AICS ML Segmentation (One-Way) Mirror

ipfx

computes intrinsic cell features from intracellular electrophysiology data

brain_observatory_examples

Gallery of visualizations and analyses of the Allen Brain Observatory

Jupyter Notebook

tasic2018analysis

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

scrattch.vis

scRNA-seq data visualization from scrattch

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.

MTG_celltypes

Human cortical cell types

SWDB_2019

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

visual_behavior_analysis

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

Jupyter Notebook

MIES

Multichannel Igor Electrophysiology Suite

BICCN_M1_Evo

Analysis for BICCN cross-species primary motor cortex project

Jupyter Notebook

SWDB_2018

Course materials for the 2018 Summer Workshop on the Dynamic Brain

Jupyter Notebook

swdb_2022

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

Jupyter Notebook

dipde

Numerical solver for coupled population density equations

neuron_morphology

Tools for working with single-neuron morphological reconstructions

cell_type_mapper

Repository for storing prototype functionality implementations for the BKP

AIBSOPT

Optical projection tomography microscope for isotropic whole-brain imaging

All-active-Workflow

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

patchseqtools

QC and cell type assignment for patch-seq transcriptomics data

biophys_optimize

Optimization of single-cell biophysically detailed models

asap-modules

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

visual_coding_2p_analysis

Visual Coding 2P analysis code

NucCellTypes

drcme

Dimensionality-reduction and classification for morphology and electrophysiology

MouseBrainHierarchy

allensdk.eye_tracking

Allen Institute mouse eye tracker.

octoDAC

8 channel analog output shield for Arduino Uno

nomenclature

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

scrattch.io

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

mfishtools

Building Gene Sets and Mapping mFISH Data

SWDB_2017

course materials for the 2017 Summer Workshop on the Dynamic Brain

aifi-swanson-teaseq

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

ophys_etl_pipelines

Pipelines and modules for processing optical physiology data

scrattch.bigcat

iterative clustering pipeline of big single cell datasets.

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

open_dataset_tools

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

Jupyter Notebook

pytic

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

All-active-Manuscript

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

Jupyter Notebook

swdb_2017_tools

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

Jupyter Notebook

ImageryClient

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

coupledAE-patchseq

Multimodal data alignment and cell type analysis with coupled autoencoders.

Jupyter Notebook

piTEAM

Parallel Imaging Pipeline Using Transmission Electron Automated Microscopes (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

render-python

A python interface for render

GLIF_Teeter_et_al_2018

Analysis code for Teeter et al 2018 Nature Communications Manuscript

coupledAE

Repository for NeurIPS 2019 paper

Jupyter Notebook

neuropixels_platform_paper

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

Jupyter Notebook

U-DAGAN

Unsupervised data augmentation using GANs.

3D-atlas-reverse-mapping

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

Jupyter Notebook

swdb_2019_student

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

Jupyter Notebook

arkhipov2018_layer4

Modeling code related to Arkhipov 2018 publication

stpt_registration

STPT registration methods

CCF_Tutorial

Jupyter Notebook

swdb_2021

Jupyter Notebook

patchseq_human_L23

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

DashDataFrame

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

L5_VEN

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

CCFv3_Volumetric_Analysis

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

OFS-EM-Connectomics

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

Jupyter Notebook

human_cross_areal

Human cellular diversity across cortex

Jupyter Notebook

CNS_2021

Resources for Allen Instutite tutorials presented at CNS 2021

Jupyter Notebook

deepinterpolation_nextflow

em_coregistration

align a 3D data set to another

croissant

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

ephys_pink_noise

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.

em_stitch

EM microscopy lens correction

neuropixels_protocol_resources

Notebooks and design files for Allen Brain Observatory experimental procedures

Jupyter Notebook

bmtk-workshop

Jupyter Notebook

Great_Ape_MTG

snRNA-seq of temporal cortex in great apes

Jupyter Notebook

brain_observatory_utilities

A repository for analysis tools for data available from the AllenSDK

Jupyter Notebook

skeleton_plot

tools for plotting swc and meshparty skeletons

Jupyter Notebook

deepinterpolation_paper

Guidebook

GLIFS_ASC

GLIFS plus after spike currents

patchseq_human_L1

supporting data and code for human L1 patchSeq manuscript

Jupyter Notebook

jem

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

ophys_nway_matching

cortical_coordinates

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

Contrast_Analysis

BigFeta

Big FeaTure Aligner: a scalable solution for feature alignment

PeptidergicNetworks

Repository for Smith et al. 2019

bonsai_workflows

A collection of bonsai workflows developed at the Allen Institute

Jupyter Notebook