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.

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