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.

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

Per-project pipelines

Project name	Modalities	Pipeline repository
Dynamic foraging	behavior, behavior-videos, fib	github, code ocean