AllenInstitute/npc_sessions

Tools for accessing and packaging data from behavior and epyhys sessions from the Mindscope Neuropixels team, in the cloud.

Language: Jupyter Notebook - Size: 28.6 MB - Last synced: about 13 hours ago - Pushed: 12 days ago - Stars: 1 - Forks: 1

AllenInstitute/npc_shields

Tools for Neuropixels probe insertion into SHIELD implants: providing suggested targets, recording actual insertions, storing notes.

Language: Python - Size: 1.15 MB - Last synced: about 24 hours ago - Pushed: 1 day ago - Stars: 0 - Forks: 0

AllenInstitute/MinneTaskQueue

collection of scripts for running large scale tasks on Microns Data

Language: Python - Size: 51.8 KB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 1 - Forks: 0

AllenInstitute/openscope_psycode Fork of AllenInstitute/openscope_sequencelearning_stim

This repository contains the stimulus behind the PsyCode project

Language: Python - Size: 6.3 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

AllenInstitute/bmtk

Brain Modeling Toolkit

Language: Python - Size: 221 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 257 - Forks: 84

AllenInstitute/ACE

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

Language: R - Size: 24.7 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 1 - Forks: 1

AllenInstitute/sourcesep

Language: Jupyter Notebook - Size: 64.2 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 0 - Forks: 0

AllenInstitute/np_codeocean

Tools for uploading and interacting with Mindscope Neuropixels experiments on Code Ocean

Language: Python - Size: 426 KB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 0 - Forks: 2

AllenInstitute/Perisomatic_Based_CellTyping Fork of lelabbady/Perisomatic_Based_CellTyping

Repository to accompany the manuscript Perisomatic Ultrastructure Efficiently Classifies Cells in Mouse Cortex.

Language: Jupyter Notebook - Size: 45.4 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 0 - Forks: 0

AllenInstitute/Extract_Somatic_Features

A pipeline to extract soma and nucleus features from the segmentation of precomputed EM datasets.

Language: Jupyter Notebook - Size: 18.7 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 0 - Forks: 0

AllenInstitute/Bulk-RNA-Snakeline

Language: Python - Size: 607 KB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 0 - Forks: 0

AllenInstitute/np_tools

General-purpose tools for common tasks encountered in Mindscope Neuropixels workflows.

Language: Python - Size: 253 KB - Last synced: about 13 hours ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

AllenInstitute/neuroanalysis Fork of campagnola/neuroanalysis

Modular analysis tools for neurophysiology data

Language: Python - Size: 1.98 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 7 - Forks: 10

AllenInstitute/ephys-analysis-tools

Code base generating formatted data tables that streamlines data analysis process for ephys production metadata.

Language: Python - Size: 288 KB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

AllenInstitute/aisynphys Fork of aiephys/multipatch_analysis

Analysis tools specific to the aiephys multipatch project.

Language: Python - Size: 57.4 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 9 - Forks: 5

AllenInstitute/np_notebooks

Language: Jupyter Notebook - Size: 10.5 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 0 - Forks: 3

AllenInstitute/np_workflows

Language: Jupyter Notebook - Size: 14.7 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 1 - Forks: 2

AllenInstitute/openscope_databook

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

Language: Python - Size: 434 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 52 - Forks: 15

AllenInstitute/npc_lims

Tools to fetch and update paths, metadata and state for Mindscope Neuropixels sessions, in the cloud.

Language: Python - Size: 1.53 MB - Last synced: about 13 hours ago - Pushed: 7 days ago - Stars: 0 - Forks: 0

AllenInstitute/aics-fms-file-explorer-app

AICS FMS File Explorer Front End

Language: TypeScript - Size: 14.1 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 2 - Forks: 1

AllenInstitute/patchseqtools

QC and cell type assignment for patch-seq transcriptomics data

Language: HTML - Size: 7.37 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 15 - Forks: 3

AllenInstitute/npc_samstim

Tools for processing stim data from Sam's DynamicRoutingTask, compatible with data in the cloud.

Language: Python - Size: 116 KB - Last synced: 12 days ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

AllenInstitute/AllenSDK

code for reading and processing Allen Institute for Brain Science data

Language: Jupyter Notebook - Size: 234 MB - Last synced: 5 days ago - Pushed: 4 months ago - Stars: 326 - Forks: 149

AllenInstitute/microns_tutorial

testing tutorial publishing

Language: Jupyter Notebook - Size: 67.5 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0

AllenInstitute/em_stitch

EM microscopy lens correction

Language: Python - Size: 86.4 MB - Last synced: 14 days ago - Pushed: about 2 months ago - Stars: 4 - Forks: 3

AllenInstitute/ndx-dynamic-routing-metadata

Language: Python - Size: 133 KB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

AllenInstitute/npc_mvr

Tools for reading raw video data from MindScope Neuropixels experiments, compatible with data in the cloud.

Language: Python - Size: 150 KB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 0

AllenInstitute/neuron_morphology

Tools for working with single-neuron morphological reconstructions

Language: Python - Size: 1.77 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 19 - Forks: 8

AllenInstitute/PyGraphTEASAR

A library for running the TEASAR algorithm on spatial graphs embedded using scipy csgraph operations.

Language: Python - Size: 52.7 KB - Last synced: 16 days ago - Pushed: about 1 year ago - Stars: 3 - Forks: 0

AllenInstitute/npc_sync

Repackaging of AllenSDK.SyncDataset with extra functionality, compatible with data in the cloud.

Language: Python - Size: 451 KB - Last synced: 16 days ago - Pushed: 17 days ago - Stars: 0 - Forks: 0

AllenInstitute/npc_ephys

Tools for accessing and processing raw ephys data, compatible with data in the cloud.

Language: Python - Size: 142 KB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 0 - Forks: 2

AllenInstitute/deepinterpolation

Language: Python - Size: 182 MB - Last synced: 17 days ago - Pushed: 3 months ago - Stars: 203 - Forks: 49

AllenInstitute/npc_stim

Tools for accessing and processing stim data, compatible with data in the cloud.

Language: Python - Size: 237 KB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 0 - Forks: 0

AllenInstitute/deepinterpolation_paper

Language: Python - Size: 303 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 3 - Forks: 1

AllenInstitute/scrattch.mapping

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

Language: R - Size: 3.83 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 5 - Forks: 2

AllenInstitute/cell_type_mapper

Repository for storing prototype functionality implementations for the BKP

Language: Python - Size: 4.75 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 9 - Forks: 2

AllenInstitute/bmark

Pilot for single cell benchmarking datasets

Language: Jupyter Notebook - Size: 49.9 MB - Last synced: 21 days ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

AllenInstitute/licking_behavior_NP

Analysis of mouse licking behavior during visually guided behavior

Language: Python - Size: 7.84 MB - Last synced: 21 days ago - Pushed: 22 days ago - Stars: 0 - Forks: 1

AllenInstitute/scrattch.bigcat

iterative clustering pipeline of big single cell datasets.

Language: R - Size: 4.13 MB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 14 - Forks: 7

AllenInstitute/BigFeta

Big FeaTure Aligner: a scalable solution for feature alignment

Language: Python - Size: 10.4 MB - Last synced: 23 days ago - Pushed: 3 months ago - Stars: 4 - Forks: 2

AllenInstitute/DevCCF_CCFv3_mapping

Code for generating analyses and figures used in Kronman et al. (doi: 10.1101/2023.09.14.557789)

Language: Python - Size: 244 KB - Last synced: 24 days ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

AllenInstitute/visual_behavior_glm

GLM for ophys df/f during visual behavior

Language: Jupyter Notebook - Size: 163 MB - Last synced: 26 days ago - Pushed: 26 days ago - Stars: 2 - Forks: 0

AllenInstitute/ecephys_spike_sorting

Modules for processing extracellular electrophysiology data from Neuropixels probes

Language: Python - Size: 6.79 MB - Last synced: 9 days ago - Pushed: 4 months ago - Stars: 97 - Forks: 86

AllenInstitute/abc_atlas_access

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

Language: Jupyter Notebook - Size: 199 MB - Last synced: 27 days ago - Pushed: about 2 months ago - Stars: 37 - Forks: 15

AllenInstitute/deep-neurographs

Neuron reconstruction framework that detects and corrects false splits in a predicted segmentation.

Language: Python - Size: 3.11 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 0

AllenInstitute/swdb_2022_python_bootcamp

Language: HTML - Size: 20.6 MB - Last synced: 29 days ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1

AllenInstitute/patchseq_human_L1

supporting data and code for human L1 patchSeq manuscript

Language: Jupyter Notebook - Size: 59.9 MB - Last synced: 29 days ago - Pushed: 9 months ago - Stars: 3 - Forks: 0

AllenInstitute/ipfx

computes intrinsic cell features from intracellular electrophysiology data

Language: Python - Size: 14.4 MB - Last synced: 29 days ago - Pushed: 5 months ago - Stars: 24 - Forks: 34

AllenInstitute/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.

Language: Python - Size: 11.4 MB - Last synced: 29 days ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

AllenInstitute/transcriptomic_clustering

improved clustering pipeline for transcriptomic data

Language: Python - Size: 420 KB - Last synced: 29 days ago - Pushed: 29 days ago - Stars: 1 - Forks: 0

AllenInstitute/GeneOrthology

CSV file and R package for collecting gene ortholog information from NCBI.

Language: R - Size: 18 MB - Last synced: 27 days ago - Pushed: 4 months ago - Stars: 4 - Forks: 0

AllenInstitute/np_audio_control

Tools for remote control of Windows system audio on Mindscope Neuropixels and Behavior rigs

Language: Python - Size: 65.4 KB - Last synced: 2 days ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

AllenInstitute/openscope_texture Fork of AllenInstitute/openscope_sequencelearning_stim

This repository contains the stimulus behind the texture project

Language: Python - Size: 398 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 1

AllenInstitute/BICCN_M1_Evo

Analysis for BICCN cross-species primary motor cortex project

Language: Jupyter Notebook - Size: 101 MB - Last synced: 3 days ago - Pushed: 3 months ago - Stars: 21 - Forks: 7

AllenInstitute/visual_behavior_analysis

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

Language: Jupyter Notebook - Size: 441 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 21 - Forks: 6

AllenInstitute/dispimdb

Language: Python - Size: 176 KB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

AllenInstitute/WholeBrainRabiesAnalysis

Language: HTML - Size: 27.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

AllenInstitute/scrattch.hicat

Hierarchical, iterative clustering for analysis of transcriptomics data in R

Language: HTML - Size: 154 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 95 - Forks: 31

AllenInstitute/openscope-barcodingstim Fork of lalwanii26/openscope-barcodingstim

Stimulus and sequence generation code for the Temporal Coding of Broadband Stimuli as a Classification Barcode OpenScope project

Language: Python - Size: 546 KB - Last synced: about 2 months ago - Pushed: 10 months ago - Stars: 1 - Forks: 1

AllenInstitute/consciousness-circlestim Fork of LydiaMarks/openscope-circlestim

Stimulus for a consciousness experiment

Language: Python - Size: 524 KB - Last synced: about 2 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

AllenInstitute/render-python

A python interface for render

Language: Python - Size: 5.55 MB - Last synced: 17 days ago - Pushed: 4 months ago - Stars: 9 - Forks: 10

AllenInstitute/chromosome-network-modeling

Language: Python - Size: 44.6 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

AllenInstitute/sonata

Collaboration between BBP and AIBS

Language: Python - Size: 139 MB - Last synced: 21 days ago - Pushed: 7 months ago - Stars: 49 - Forks: 31

AllenInstitute/mouse_connectivity_models

Python package providing mesoscale connectivity models for mouse.

Language: Python - Size: 560 MB - Last synced: about 1 month ago - Pushed: 4 months ago - Stars: 38 - Forks: 14

AllenInstitute/bonsai_workflows

A collection of bonsai workflows developed at the Allen Institute

Language: Jupyter Notebook - Size: 82.8 MB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 2 - Forks: 3

AllenInstitute/patchseq_autotrace

Execution of patchseq slice autotrace pipeline

Language: Python - Size: 21.9 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

AllenInstitute/scrattch.vis

scRNA-seq data visualization from scrattch

Language: R - Size: 104 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 22 - Forks: 2

AllenInstitute/QCR

QCR stands for Quality Control workflow for sc/sn RNA-seq data

Language: R - Size: 856 KB - Last synced: 21 days ago - Pushed: 8 months ago - Stars: 3 - Forks: 0

AllenInstitute/MOp_taxonomies_ontology

Central location for versioning and sharing of taxonomy files relevant for ontology development as part of cell type cards.

Language: HTML - Size: 15.4 MB - Last synced: 3 months ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0

AllenInstitute/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.

Language: R - Size: 23.6 MB - Last synced: 3 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 4

AllenInstitute/brspdata

Allen Institute BrainSpan Exon and Gene Expression Values

Language: R - Size: 216 MB - Last synced: 3 months ago - Pushed: over 6 years ago - Stars: 2 - Forks: 2

AllenInstitute/mfishtools

Building Gene Sets and Mapping mFISH Data

Language: HTML - Size: 2.07 MB - Last synced: 3 months ago - Pushed: 11 months ago - Stars: 14 - Forks: 5

AllenInstitute/CP_molecular_organization

Language: Jupyter Notebook - Size: 10 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

AllenInstitute/scrattch.example

Language: HTML - Size: 2.93 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

AllenInstitute/nomenclature

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

Language: HTML - Size: 2.16 MB - Last synced: 3 months ago - Pushed: about 2 years ago - Stars: 13 - Forks: 2

AllenInstitute/pytic

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

Language: Python - Size: 519 KB - Last synced: 2 days ago - Pushed: 5 months ago - Stars: 10 - Forks: 6

AllenInstitute/npc_utils

Collection of MindScope Neuropixels packages, to simplify installation and keeping versions updated.

Language: Python - Size: 850 KB - Last synced: 13 days ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

AllenInstitute/brain_observatory_utilities

A repository for analysis tools for data available from the AllenSDK

Language: Jupyter Notebook - Size: 566 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 3 - Forks: 1

AllenInstitute/dLGN_cross_species

Language: R - Size: 2.09 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

AllenInstitute/npc_io

File IO tools for MindScope Neuropixels projects in the cloud.

Language: Python - Size: 725 KB - Last synced: 23 days ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

AllenInstitute/scrattch.taxonomy

Allen Institute Taxonomy building R package

Language: HTML - Size: 750 KB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 1

AllenInstitute/hmba_image_viewer

Repository for code related to the HMBA Image Viewer project (summer 2023)

Language: Jupyter Notebook - Size: 24.6 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 2

AllenInstitute/copier-pdm-npc Fork of bjhardcastle/copier-pdm-npc

Copier template for Mindscope Neuropixels projects

Language: Jinja - Size: 218 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 1

AllenInstitute/render-python-apps

Language: Python - Size: 22.4 MB - Last synced: 4 months ago - Pushed: over 4 years ago - Stars: 3 - Forks: 1

AllenInstitute/ATExplorer

API's and Applications for ArrayTomography (AT)

Language: Pascal - Size: 537 MB - Last synced: 4 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

AllenInstitute/swdb_2021

Language: Jupyter Notebook - Size: 94.8 MB - Last synced: 4 months ago - Pushed: over 2 years ago - Stars: 5 - Forks: 20

AllenInstitute/dynamicrouting-summary

Project summary plots & tables, started for onsite retreat Jan 2024.

Language: Jupyter Notebook - Size: 3.86 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

AllenInstitute/MTG_celltypes

Human cortical cell types

Language: R - Size: 632 KB - Last synced: 3 months ago - Pushed: over 4 years ago - Stars: 21 - Forks: 7

AllenInstitute/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.

Language: Python - Size: 583 KB - Last synced: 17 days ago - Pushed: over 1 year ago - Stars: 24 - Forks: 12

AllenInstitute/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.

Language: Python - Size: 21.5 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

AllenInstitute/deepinterpolation_nextflow

Language: Python - Size: 961 KB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 4 - Forks: 1

AllenInstitute/ZeroMQ-XOP

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

Language: C - Size: 77 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 9 - Forks: 7

AllenInstitute/openai_tools

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

Language: HTML - Size: 18.6 MB - Last synced: about 2 months ago - Pushed: 12 months ago - Stars: 109 - Forks: 15

AllenInstitute/SWDB_CellTypeFunction

Day of exercises with Cell Type function

Language: HTML - Size: 42.9 MB - Last synced: 4 months ago - Pushed: 9 months ago - Stars: 1 - Forks: 4

AllenInstitute/MIES

Multichannel Igor Electrophysiology Suite

Language: IGOR Pro - Size: 434 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 19 - Forks: 6

AllenInstitute/human_patchseq_gaba

Language: HTML - Size: 29.5 MB - Last synced: 3 months ago - Pushed: 6 months ago - Stars: 2 - Forks: 1

AllenInstitute/brain_observatory_qc

Language: Jupyter Notebook - Size: 4.41 MB - Last synced: 29 days ago - Pushed: 2 months ago - Stars: 2 - Forks: 0

AllenInstitute/aics-ml-segmentation

AICS ML Segmentation (One-Way) Mirror

Language: Python - Size: 8.86 MB - Last synced: 25 days ago - Pushed: about 3 years ago - Stars: 26 - Forks: 6

AllenInstitute/pycilium

Language: Python - Size: 15.6 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

AllenInstitute/sptx_ccf_registration

Spatial Transcriptomics - CCF Registration

Language: Python - Size: 9.2 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 0