Allen Institute's repositories
openscope_databook
OpenScope databook: a collaborative, versioned, data-centric collection of foundational analyses for reproducible systems neuroscience 🐁🧠🔬🖥️📈
scrattch.bigcat
iterative clustering pipeline of big single cell datasets.
visual_behavior_analysis
Python package for analyzing behavioral data for Brain Observatory: Visual Behavior
ophys_etl_pipelines
Pipelines and modules for processing optical physiology data
neuroanalysis
Modular analysis tools for neurophysiology data
transcriptomic_clustering
improved clustering pipeline for transcriptomic data
deep-neurographs
Deep-Neurographs is a Python module that utilizes machine learning to detect and correct false splits in a predicted neuron segmentation.
mtrain_regimens
Repository to track training stages and regimens for visual behavior
microns_tutorial
MICrONS databook and analysis tutorials
openscope_texture
This repository contains the stimulus behind the texture project
skeleton_keychain
This package links together commands from the skeleton-keys package to run typical steps of feature calculation/file generation pipelines on a slurm hpc system.
BarCounter-release
BarCounter DNA barcode quantification
ephys-analysis-tools
Code base generating formatted data tables that streamlines data analysis process for ephys production metadata.
Extract_Somatic_Features
A pipeline to extract soma and nucleus features from the segmentation of precomputed EM datasets.
featureExtractionParty
Repo for extracting features from EM meshes
npc_shields
Tools for Neuropixels probe insertion into SHIELD implants: providing suggested targets, recording actual insertions, storing notes.
npc_sync
Repackaging of AllenSDK.SyncDataset with extra functionality, compatible with data in the cloud.
SHIELD_Dynamic_Gating_Analysis
Code to analyze dynamic gating nwbs with data collected using the SHIELD implant
syringepump
python code for syringepump.com syringe pumps
TEM_comms
Pigeon messages for the next generation TEM imaging system