Building Pipelines
Creating a pipeline
There are two ways to create a pipeline:1. AI-generated pipelines
The fastest way to create a pipeline is to describe what you want in natural language:- Open the AI agent prompt bar
- Describe your goal: “Create a pipeline to segment cells, count them, and export measurements as CSV”
- The agent generates a pipeline definition with properly configured steps
- Review and edit the pipeline in the pipeline builder
- Run it
2. Manual pipeline building
The pipeline builder uses a visual DAG (directed acyclic graph) editor built on ReactFlow:- Open a pane in Pipeline Builder mode
- Drag nodes from the Node Palette onto the canvas
- Connect nodes by dragging between ports
- Select a node to configure its parameters in the Node Inspector
- Use undo/redo for editing history
- Run the pipeline
Step types
Client steps (browser-based)
Client steps run in your browser with no server cost:| Operation | Category | Description |
|---|---|---|
| Threshold | Filter | Binary thresholding |
| Brightness/Contrast | Filter | Adjust image brightness and contrast |
| Gaussian Blur | Filter | Apply Gaussian smoothing |
| Edge Detection | Filter | Detect edges (Sobel/Canny) |
| Color Transform | Transform | Convert between color spaces |
| Crop | Transform | Crop to region of interest |
| Resize | Transform | Resize image dimensions |
Server steps (GPU-powered)
Server steps run models on cloud GPUs:| Model | Description |
|---|---|
| sam3 | Segment Anything — universal segmentation |
| deeplabcut | Pose estimation — animal tracking |
| suite2p | Calcium imaging analysis |
| spikeinterface | Spike sorting |
| plantcv | Plant phenotyping |
| sextractor | Astronomical source detection |
Running a pipeline
- Ensure your input file is loaded in the viewer
- Click Run Pipeline in the pipeline builder
- Steps execute sequentially — client steps run instantly, server steps submit GPU jobs
- Progress is shown per-step with logs
- Results appear in the viewer as they complete
Pipeline output
Each step produces outputs that can be:- Displayed in the viewer — masks, overlays, annotated images
- Passed to the next step — intermediate results flow through the pipeline
- Downloaded — final outputs are available as files (CSV, NPY, PNG, etc.)