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3d-atlas-reverse-mapping

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

abc_atlas_access

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

acq4

Data acquisition for patch clamp ephys / optogenetics / imaging experiments

agedbrain

Code and files for reproducing the analysis presented in "Neuropathological and transcriptomic characteristics of the aged brain," the platform paper for the Aging, Dementia, and TBI Study.

aibs-smartspim-flythrough

CodeOcean tool for making videos of SmartSPIM data sets

aibs_synapse

STP model implementation for NEST (neural simulation platform)

aibsopt

Optical projection tomography microscope for isotropic whole-brain imaging

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.

aics-fms-file-explorer-app

AICS FMS File Explorer Front End

aics-ml-segmentation

AICS ML Segmentation (One-Way) Mirror

aics-segmentation

AICS Segmentation (One-Way) Mirror

aifi-swanson-icicleseq

Moved to aifi-swanson-teaseq

aifi-swanson-teaseq

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

aisynphys

Analysis tools specific to the aiephys multipatch project.

all-active-manuscript

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

all-active-workflow

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

alleninstitute.github.io

allensdk

code for reading and processing Allen Institute for Brain Science data

allensdk.eye_tracking

Allen Institute mouse eye tracker.

anndata

Annotated data.

anndata_dissector

Utilities for slicing and dicing h5ad files without overwhelming your system's memory

annotation_comparison

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

archr

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

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.

arkhipov2018_layer4

Modeling code related to Arkhipov 2018 publication

asap-modules

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

ateam-tools

Shared model-based simulation and analysis tools (ranging from single-neuron to networks) as well as more general model/experiment analysis software (ephys, morphology, transcriptomics) of the Anastassiou team at the Allen Institute for Brain Science.

atexplorer

API's and Applications for ArrayTomography (AT)

atlas_helper_tools

A collection of notebooks and code snippets for accessing and using atlas related resources

atlasplot

Reproducible Plots for the Allen Institutes Brain Atlases