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AllenNeuralDynamics

236 indexed repositories · View on GitHub

aind-ephys-pipeline
AIND pipeline for processing extracellular electrophysiology data

Nextflow · 41 stars
aind-data-schema
A library that defines AIND data schema and validates JSON.

Python · 34 stars
openscope-community-predictive-processing
This repository serves as a hub for community-driven contributions, documentation, and project tracking of the OpenScope Predictive Proce...

Python · 26 stars
aind-ephys-spikesort-kilosort25-full
CodeOcean capsule for full electrophysiology analysis pipeline using Kilosort2.5 via SpikeInterface.

Python · 14 stars
aind-large-scale-cellpose
Large-scale cell segmentation with cellpose.

Python · 10 stars
Rhapso
An open-source Python toolkit for large-scale fluorescence microscopy data alignment and fusion.

Python · 9 stars
dynamic-foraging-task
Bonsai/Harp workflow for Dynamic Foraging with Python GUI for visualization and control

Python · 7 stars
aind-smartspim-pipeline
Repository that hosts the SmartSPIM pipeline code

Nextflow · 6 stars
TigerASI
a lightweight python interface for ASI brand Tiger Controllers

Python · 5 stars
wavpack-numcodecs
Numcodecs implementation of the WavPack audio codec

C · 5 stars
anivia
Fork of VGG VIA to better support annotation of animal pose images

JavaScript · 4 stars
harp.device.treadmill-driver
0326: a Harp-compatible device for controlling an instrumented mouse treadmill

Jupyter Notebook · 4 stars
voxel-classic
General purpose microscope control repository

Python · 4 stars
view
Model/View for exa-spim

Python · 4 stars
harp.device.lickety-split
0360: an ephys-compliant capacitive lick detector

C++ · 4 stars
runze-control
Python Driver for Aurora Pro Scientific (aka Runze Fluid) syringe pumps

Python · 4 stars
parallax
Automatic detection of probe position from multiple camera views

Python · 4 stars
aind-SmartSPIM-segmentation
segmentation module for SmartSPIM cloud pipeline

Python · 4 stars
aind-smartspim-stitch
Stitching and fusion pipeline in the cloud

Python · 4 stars
aind-smartspim-ccf-registration
Registration of lightsheet whole brain images to the Allen CCF V3 Atlas

Python · 4 stars
216 more repositories live on View on GitHub

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1400 issues indexed so far

Generate argparse ArgumentParser from app-panel.json Open

enhancement

AllenNeuralDynamics/aind-codeocean-utils#30 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Update badges workflow is broken Open

AllenNeuralDynamics/aind-codeocean-utils#34 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
helper to generate model metadata for CO mlflow model Open

enhancement

AllenNeuralDynamics/aind-codeocean-utils#37 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Make inputs generic Open

AllenNeuralDynamics/aind-nwb-combine#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Validate using other acquisition systems Open

AllenNeuralDynamics/aind-nwb-combine#5 · 3 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Ensure public members are correctly cased Open

AllenNeuralDynamics/AllenNeuralDynamics.HamamatsuCamera#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Consider automatically publishing package to nuget Open

AllenNeuralDynamics/AllenNeuralDynamics.HamamatsuCamera#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
FYI: Major refactoring ahead Open

AllenNeuralDynamics/neuron-tracing-utils#3 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Allow basic viewer settings NG manipulation, tool use, defaults in the front end. Open

AllenNeuralDynamics/neuroglancer-chat#5 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 13, 2026
create agent status indicators Open

AllenNeuralDynamics/neuroglancer-chat#6 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
modify source images Open

AllenNeuralDynamics/neuroglancer-chat#7 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
upload csv table duplicates and file size limits Open

AllenNeuralDynamics/neuroglancer-chat#8 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
mixing matrix heatmap labels unclear Open

AllenNeuralDynamics/see-spot#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Selected spots table columns and spot info pop up could be more specific and consistent Open

AllenNeuralDynamics/see-spot#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
dist and r value filtering doesnt seem to work / could be optimized Open

AllenNeuralDynamics/see-spot#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Ability to view mixed spot data Open

AllenNeuralDynamics/see-spot#5 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Ability to color spots by original channel instead of reassigned channel Open

AllenNeuralDynamics/see-spot#6 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
For future consideration - including coexpression heatmap for genes in reference dataset Open

AllenNeuralDynamics/see-spot#7 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
identify spatially overlapping spots Open

AllenNeuralDynamics/see-spot#8 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Update SeeSpot to use Independent Tile NG links Open

AllenNeuralDynamics/see-spot#11 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Meshparty meshwork as base class for NeuronData Open

AllenNeuralDynamics/aind-neuron-reconstruction-io#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
More lexible metadata framework Open

AllenNeuralDynamics/aind-neuron-reconstruction-io#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
use post-run automation capsule to register results Open

AllenNeuralDynamics/nmcp-snapshot-capsule#2 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
automatically query for raw/fused/reconstruction asset inputs Open

AllenNeuralDynamics/nmcp-snapshot-capsule#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Use portal API to automatically register generated snapshot to portal Open

enhancement

AllenNeuralDynamics/nmcp-snapshot-capsule#7 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Upgrade aind-codeocean-pipeline-monitor to latest version Open

AllenNeuralDynamics/aind-co-pipeline-monitor-capsule-all-users#1 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Detect if device is in passthrough mode Open

AllenNeuralDynamics/harp.device.cuttlefish#6 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Schedule should have the option of referencing Harp Time Open

AllenNeuralDynamics/harp.device.cuttlefish#9 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
`PortState` change event not implemented Open

good first issue

AllenNeuralDynamics/harp.device.cuttlefish#17 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Send Harp EVENT if Schedule cannot be implemented Open

AllenNeuralDynamics/harp.device.cuttlefish#19 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Disabling Task Should Kill Port Output Open

AllenNeuralDynamics/harp.device.cuttlefish#24 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Interface Overhaul Open

MVP

AllenNeuralDynamics/harp.device.cuttlefish#31 · 4 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Disable PWM when device goes into idle mode Open

firmware

AllenNeuralDynamics/harp.device.cuttlefish#33 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Start individual PWM Channels individually Open

AllenNeuralDynamics/harp.device.cuttlefish#34 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Add a changelog.md Open

AllenNeuralDynamics/harp.device.cuttlefish#36 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
BNC Connectors are hard to attach/remove Open

hardware

AllenNeuralDynamics/harp.device.cuttlefish#38 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Disable output when device goes to IDLE Open

AllenNeuralDynamics/harp.device.cuttlefish#43 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Consider using the pydantic-settings package Open

AllenNeuralDynamics/aind-metadata-extractor#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Update `models/fip.json` to include `acquisition_type` Open

AllenNeuralDynamics/aind-metadata-extractor#34 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Update `models/fip.json` to specify patch_cord/fiber connections Open

AllenNeuralDynamics/aind-metadata-extractor#35 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Update `models/fip.json` to specify `code` fields Open

AllenNeuralDynamics/aind-metadata-extractor#36 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Incorrect run method in readme Open

AllenNeuralDynamics/aind-metadata-extractor#50 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Force developers to name paired unit fields properly Open

AllenNeuralDynamics/aind-flake8-extensions#4 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Radial Correction Validation for current Imaging Objectives Open

AllenNeuralDynamics/aind-z1-radial-correction#5 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
linting fails due to aind-hcr-data-transformation requirement of 3.10 python Open

AllenNeuralDynamics/aind-z1-radial-correction#8 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Translation metadata wrong in zarr v2 Open

AllenNeuralDynamics/aind-z1-radial-correction#11 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Update processing to v2 aind-data-schema Open

AllenNeuralDynamics/aind-z1-radial-correction#14 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Set overlap area to 0 in all axis when it's None Open

bug

AllenNeuralDynamics/aind-large-scale-prediction#5 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Add QC Open

AllenNeuralDynamics/suitefp#3 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Migrate Po-Chen's code Open

AllenNeuralDynamics/aind-spurious-correlation#1 · 1 comment · 0 reactions · 2 assignees · Indexed Sep 13, 2026

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