Allen Institute

Repositories

• MIES

  Multichannel Igor Electrophysiology Suite

  electrophysiology igor-pro supported
  IGOR Pro 3 9 123 (1 issue needs help) 5 Updated Sep 19, 2020

• aics-fms-file-explorer-app

  AICS FMS File Explorer Front End
  TypeScript 1 0 0 0 Updated Sep 18, 2020

• AllenSDK

  code for reading and processing Allen Institute for Brain Science data

  bioinformatics scientific
  Jupyter Notebook 98 178 291 (4 issues need help) 10 Updated Sep 18, 2020

• aisynphys

  Forked from aiephys/multipatch_analysis

  Analysis tools specific to the aiephys multipatch project.
  Python 17 2 1 0 Updated Sep 18, 2020

• sonata

  Collaboration between BBP and AIBS
  Python BSD-3-Clause 21 24 32 5 Updated Sep 18, 2020

• brain_observatory_examples

  Gallery of visualizations and analyses of the Allen Brain Observatory
  Jupyter Notebook 5 9 1 1 Updated Sep 17, 2020

• GLIF2NEST

  GLIF (Generalized Leaky Integrate and Fire) Models for NEST Simulator
  C++ GPL-2.0 1 0 2 1 Updated Sep 17, 2020

• neuroanalysis

  Forked from campagnola/neuroanalysis

  Modular analysis tools for neurophysiology data
  Python MIT 17 4 1 1 Updated Sep 17, 2020

• ipfx

  computes intrinsic cell features from intracellular electrophysiology data
  Python 19 9 43 4 Updated Sep 17, 2020

• visual_behavior_analysis

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

  python behavior neuroscience psychology psychophysics
  Jupyter Notebook 0 3 57 1 Updated Sep 17, 2020

• croissant

  Classifying regions of interest in mouse brain as cell or not cell
  Python 1 3 10 1 Updated Sep 16, 2020

• bmtk

  Brain Modeling Toolkit

  python simulation modeling neuroscience neural-networks neuroinformatics neuron
  Python BSD-3-Clause 56 144 24 3 Updated Sep 16, 2020

• ophys_nway_matching
  Python 0 0 4 0 Updated Sep 16, 2020

• U-DAGAN

  Unsupervised data augmentation using GANs.
  Python 1 1 0 0 Updated Sep 16, 2020

• volume-viewer
  JavaScript 3 76 0 0 Updated Sep 14, 2020

• nomenclature

  This repository contains code to generate standardized cell type nomenclature from an R "dendrogram".
  HTML 0 3 0 0 Updated Sep 14, 2020

• TileQC

  Tile Quality Control for piTEAM
  Python 0 0 0 0 Updated Sep 11, 2020

• AIBSOPT

  Optical projection tomography microscope for isotropic whole-brain imaging
  Python 0 8 0 0 Updated Sep 11, 2020

• aifi-swanson-icicleseq

  Code related to Swanson, et. al. for scATAC-seq and ICICLE-seq data processing, analysis and visualization
  Python 0 1 0 0 Updated Sep 11, 2020

• jem

  Repository containing JEM (JSON Electrophysiology Metadata), a web-form for logging metadata during slice electrophysiology experiments.
  HTML 3 2 0 1 Updated Sep 10, 2020

• segmentation-labeling-app

  Data pipeline and UI for human labeling of putative ROIs from 2p cell segmentations
  Python 0 0 11 1 Updated Sep 9, 2020

• 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.
  R GPL-2.0 4 0 0 1 Updated Sep 8, 2020

• human_neuron_Ih

  This repository contains the simulation code to run single neuron simulations in the early version of bmtk (https://github.com/AllenInstitute/bmtk)
  Python 1 0 0 0 Updated Sep 8, 2020

• All-active-Manuscript

  Code for reproducing the figures presented in: Single-neuron models linking electrophysiology, morphology and transcriptomics across cortical cell types
  Jupyter Notebook 1 1 0 0 Updated Sep 4, 2020

• plaque_map

  Code for generating plaque density maps
  Python 1 1 0 0 Updated Sep 3, 2020

• em_coregistration

  align a 3D data set to another
  Python 4 2 0 0 Updated Sep 3, 2020

• data_ingest

  The Allen Institute's data ingest system
  Python 0 0 0 0 Updated Sep 2, 2020

• patchseq_human_L23

  Code for reproducing the analyses presented in "Human cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neurons".
  HTML 2 1 0 0 Updated Sep 2, 2020

• All-active-Workflow

  Creating the code base for All-active Model generation written on top of Bluepyopt
  Python 0 7 1 0 Updated Sep 1, 2020

• ecephys_spike_sorting

  Modules for processing extracellular electrophysiology data from Neuropixels probes

  python3 electrophysiology spikes analysis-pipeline
  Python 13 24 3 0 Updated Aug 31, 2020