OpenHCS for imaging scientists

This section is for scientists who want to assess OpenHCS, complete a first workflow, and then use it on microscopy data without starting from Python.

Start here

Read What is OpenHCS? for the purpose and fit of OpenHCS.
Use Install and start OpenHCS to install and launch it.
Complete Your first plate workflow, a bounded first-workflow tutorial with visible checkpoints.

Learn by doing

Your first plate workflow: Generate a synthetic plate, compile the included eight-step pipeline, run it, and inspect the result. Follow this one path before adapting OpenHCS to your own data.

Complete a task

Loading and naming image sources — identify and name microscopy inputs.
Install and start OpenHCS — install, launch, verify, or update OpenHCS.
Troubleshooting and FAQ — recover from common launch, source, compilation, and viewer problems.
User guide — edit pipelines, functions, viewers, results, and local agent integrations.

Look up facts

Desktop interface — desktop windows and controls.
Configuration fields — exact configuration fields, defaults, and accepted values.
Glossary — microscopy and OpenHCS terminology.

Understand the workflow

Domain Expert Onboarding — decide whether OpenHCS fits your data and analysis goal.
Configuration and inheritance — understand configuration scopes, inheritance, and resolution.
Domain fundamentals — understand why source dimensions, compilation, and typed results matter.
Pipelines and steps — understand the pipeline declaration model.