> ## Documentation Index
> Fetch the complete documentation index at: https://docs.biom.science/llms.txt
> Use this file to discover all available pages before exploring further.

# Pipelines Overview

> Chain multiple analysis steps into automated workflows.

# Pipelines

Pipelines let you chain multiple analysis steps into automated workflows. You can build pipelines visually in the pipeline builder, or let the AI agent generate one from a natural language description.

## What is a pipeline?

A pipeline is an ordered sequence of processing steps that run on your data. Each step can be:

* **Client-side** — image processing operations that run in your browser (thresholding, filtering, transforms)
* **Server-side** — model execution on GPU (SAM3 segmentation, DeepLabCut tracking, etc.)

Steps are connected so that the output of one step feeds into the next.

## Example pipelines

### Cell counting pipeline

1. **Threshold** (client) → binarize the image
2. **SAM3 segmentation** (server) → detect all cells
3. **Count & measure** (client) → count cells and compute statistics

### Animal tracking pipeline

1. **DeepLabCut** (server) → detect keypoints per frame
2. **Export CSV** (client) → tabular coordinates for downstream analysis

### Calcium imaging pipeline

1. **Suite2p** (server) → motion correction, ROI detection, spike deconvolution
2. **Visualization** (client) → plot fluorescence traces

## Pipeline pane

Pipelines run in a dedicated **Pipeline Builder** pane type. You can:

* Switch any pane to pipeline builder mode
* Drag and drop steps to reorder them
* Configure parameters for each step
* Run the pipeline and view results inline

See [Building Pipelines](/pipelines/building-pipelines) for a step-by-step guide.