Scientific Computing Teams¶
Data Infrastructure¶
Data Infrastructure maintains the core services in AIND.
Some of the major core services:
aind-data-transfer-service
FastAPI service to run data compression and transfer jobs on the HPC
link | readthedoc | repo
aind-metadata-service
REST service to retrieve metadata from AIND databases
link | readthedoc | repo
aind-data-access-api
Library to interface with AIND databases
tutorial | readthedoc | repo
aind-data-asset-indexer
Index jobs for AIND metadata in AWS DocumentDB and S3
Data & Outreach¶
The Data & Outreach team is responsible for our open science. It maintains the data schema, the metadata chatbot, and associated downstream tools and organizes and hosts workshops and other outreach events.
aind-data-schema
Metadata schema for neuroscience
readthedoc | repo | registries repo
aind-metadata-mapper
Repository to help gather and map metadata from different sources
aind-metadata_mcp
MCP for querying the metadata DocDB
Outreach¶
SWDB Data Book
Data book for the SWDB course
Public Collections
Workshop materials
Physiology & Behavior¶
The Physiology & Behavior team maintains the pipelines that process each modality of data asset that we acquire in AIND. Details can be found in Process data.
Image Processing¶
The Image Processing team develops and maintains pipelines for processing lightsheet microscopy data across multiple imaging platforms and video pose tracking. For internal users see also this overview doc.
Behavior-Videos
behavior-video-inference-pipeline
Smartspim
Exaspim
exaspim-flatfield-correction | aind-exaspim-neuron-segmentation | aind-exaspim-soma-detection | aind-exaspim-ccf-registration | exaSPIM_register_swc_to_ccf
Z1 (HCR and Proteomics)
aind-z1-radial-correction | aind-z1-camera-alignment | aind-z1-spot-detection | aind-hcr-r2r-registration | hcr-czitile-utils | aind-hcr-data-transformation | aind-proteomics-stitch
Proteomics
aind-proteomics-image-translator
General Lightsheet
Resources for SWEs¶
For research software engineers, Good Research Code is a good primer.