Your first plate workflow

In this tutorial you will generate a bounded synthetic microscopy plate, use the pipeline supplied with it, compile the analysis, and inspect the completed result. You do not need your own data or Python code.

Before you begin

Install the desktop application with Napari support. The Windows and macOS installers include it. For a manual Python installation, use python -m pip install "openhcs[gui,napari]".

Launch openhcs. You should see Plate Manager on the left and Pipeline Editor on the right.

Generate the example plate

Choose View > Generate Synthetic Plate.
Leave the generated parameters at their defaults and leave Output Directory set to <temp directory>.
Select Generate Plate.

After the dialog closes, a new plate appears in Plate Manager and Pipeline Editor shows the supplied eight-step workflow. The first step is Image Enhancement Processing and the final step is Cell Counting. These visible changes confirm that both the data and its pipeline were created.

OpenHCS Synthetic Plate Generator with image and plate controls — Synthetic Plate Generator

Typed controls for generating a reproducible microscopy test plate.

Initialise the source data

Select the generated plate row.
Select Init in Plate Manager.
Wait for initialisation to finish.

When initialisation succeeds, Compile becomes available. Open the metadata viewer if you want to confirm the discovered wells, sites, channels, and Z planes before continuing.

OpenHCS plate viewer showing detected image and axis metadata — Plate metadata

Detected source format, image inventory, and dimensional metadata.

Inspect the supplied pipeline

Read the Pipeline Editor from top to bottom. The workflow normalises the source images, combines channels, projects Z planes, computes tile positions, assembles the sites, and counts cells. Select any step to see its declared function and configuration, but do not change values during this tutorial.

Compile the workflow

Keep the generated plate selected.
Select Compile.
Wait for compilation to finish.

Compilation checks the source dimensions and the requirements of all eight steps before processing begins. A successful compile enables Run. If an error is reported, fix the first error before continuing rather than running a partially valid workflow.

OpenHCS main window with one synthetic plate selected and its eight pipeline steps visible — Start with a complete synthetic plate and pipeline

The generated plate is selected in Plate Manager, while Pipeline Editor keeps the eight supplied steps together after initialisation and compilation.

Run and inspect the result

Select Run.
Watch the status and progress surfaces while the plate is processed.
Wait for the run to complete and for the detached Napari window to settle.
Inspect the streamed cell-count result in Napari.
Back in OpenHCS, select Results to inspect the available measurement snapshot.

OpenHCS live results window showing cell measurements and provenance — Live measurement results

Retained per-object measurements with execution and axis provenance.

You have now completed the same lifecycle used for real data: add a source, initialise it, inspect its pipeline, compile, run, and review the result.

Continue with your own data

Use Domain Expert Onboarding to collect the source and biological facts needed for a real workflow.
Use Loading and naming image sources to map your files and dimensions.
Use Real-time visualization to choose which scientific results should be streamed for review.
Read Data dimensions and execution axes when adapting the example’s site, channel, or Z behaviour.