OpenHCS documentation

OpenHCS is designed for imaging scientists and research software teams that need to turn plate-based microscopy data into measurements they can review and rerun. It keeps source selection, processing steps, and result definitions in one validated pipeline across the desktop GUI, Python, supported CellProfiler imports, and local agents.

OpenHCS Plate Manager with seven assay plates loaded, including CellProfiler Comet Assay and Wound Healing examples — Seven assay plates, one workspace

Five deterministic examples and two imported CellProfiler workflows retain independent state in one session.

Is OpenHCS right for your work?

Start with Domain Expert Onboarding if your data is organised by plates, wells, sites, channels, Z planes, or time points and you need a repeatable analysis rather than a one-off manual inspection. It explains where OpenHCS fits and what information to collect before building a pipeline.

Choose by what you need now

Learn by doing — tutorial: Follow Your first plate workflow to generate a bounded synthetic plate, compile its included pipeline, run it, and inspect the result. This is the shortest path to a complete first workflow.
Complete a task — how-to guides: Use Install and start OpenHCS to install and launch OpenHCS, then choose a task from User guide or Integration boundaries. These pages assume you know the outcome you need.
Look up exact facts — reference: Use Public API orientation for the supported Python boundary, Configuration fields for configuration fields, Dimensionality and measurement capabilities for plane-local and volumetric analysis capabilities, and Glossary for terminology.
Understand the model — explanation: Read Core Concepts for the scientific and pipeline model and Configuration and inheritance for configuration scopes and inheritance. Maintainers and integrators should continue with Architecture quick start and Architecture and ownership for ownership and runtime boundaries.