Process data

Scientific computing is currently re-organizing pipelines to be per-modality, rather than per-project.

Pipeline development requirements are documented in Pipeline development and the pipeline versioning policy is documented in Versioning pipelines.

For deployment across Code Ocean, local Docker, and SLURM, see Deploying pipelines across backends. The pophys implementation record describes the current candidate-image work and the remaining deployment requirements.

Per-modality physiology pipelines

Modality	Modalities	Pipeline repository
Barcoded anatomy resolved by sequencing	barseq
Brightfield microscopy	brightfield
Confocal microscopy	confocal
Extracellular electrophysiology	ecephys	aind-ephys-pipeline
Electron microscopy	EM
Electromyography	EMG
Fiber photometry	fib	aind-fiber-photometry-harp-pipeline
Fluorescence micro-optical sectioning tomography	fMOST
Intracellular electrophysiology	icephys
Intrinsic signal imaging	ISI	isi_segmentation
Multiplexed analysis of projections by sequencing	MAPseq
Multiplexed error-robust fluorescence in situ hybridization	merfish
Magnetic resonance imaging	MRI
Planar optical physiology	pophys	aind-pophys-pipeline
Single cell RNA sequencing	scRNAseq
Random access projection microscopy	slap2
Selective plane illumination microscopy	SPIM
Serial two-photon tomography	STPT

Behavior pipelines

Behavior	Modalities	Pipeline repository
Patch foraging behavior	behavior, behavior-videos	aind-vr-foraging-pipeline
Camstim/Sync Behavior	behavior, behavior-videos	aind-behavior-camstim-pipeline
Dynamic Foraging Behavior	behavior, behavior-videos	dynamic-foraging-processing-pipeline

Per-project pipelines

Project name	Modalities	Pipeline repository
Dynamic foraging (legacy combined behavior + fiber)	behavior, behavior-videos, fib	github, code ocean (release)

The Dynamic Foraging entry above is the legacy combined behavior + fiber photometry pipeline, for sessions acquired on the pre-HARP/FIP systems (v1 metadata schema) that are being phased out starting in the summer of 2026. Despite the aind-fiber-photometry-pipeline repo name, it processes both behavior and fiber. New fiber-only acquisition is processed by aind-fiber-photometry-harp-pipeline (the Fiber photometry row above). The Code Ocean link points to the released pipeline, which automatically resolves to the latest released version