OpenHCS documentation

OpenHCS is a bioimage-analysis platform for high-content screening. It turns pipeline declarations into validated, per-plate execution plans and runs them across microscopy datasets using CPU or GPU processing libraries.

Choose a path

Using OpenHCS

Start with Getting started, then use the User guide for task-oriented workflows.

Understanding the model

Start with the Architecture quick start, then use Core Concepts for pipelines, steps, dimensions, sources, and processing semantics.

Extending or maintaining OpenHCS

Use Developer guide for contribution workflows and Architecture reference for system boundaries and invariants.

Quick start

OpenHCS requires Python 3.11 or newer. Install and launch the desktop GUI with:

python -m pip install "openhcs[gui]"
openhcs

Viewer integrations are optional:

python -m pip install "openhcs[gui,napari]"  # Napari
python -m pip install "openhcs[gui,fiji]"    # Fiji/ImageJ
python -m pip install "openhcs[gui,viz]"     # Both

The Textual terminal interface is deprecated and is not part of the published package.

System at a glance

OpenHCS uses ordinary Python declarations at its public boundary:

PipelineConfig + list[FunctionStep]
    -> ObjectState resolution
    -> StepSnapshot + CompilationSession
    -> typed CompiledStepPlan objects
    -> CompiledExecutionBundle
    -> runtime values, artifacts, and materialized outputs

CellProfiler .cppipe files lower directly into the same PipelineConfig and FunctionStep declarations. The compiler resolves configuration once and derives source, artifact, memory, and execution plans from the authoritative declarations.

Documentation

Getting started

• Getting started
  • Requirements
  • Install OpenHCS
  • Build a pipeline in the GUI
  • Import a CellProfiler pipeline
  • Important processing terms
  • Next steps
• OpenHCS for biologists
  • User guides

Concepts

• Core Concepts
• Understanding the Domain
  • Domain fundamentals
  • Core building blocks
• Processing System
  • Function library
  • Storage and materialization
  • Data-type conversion configuration
• Practical Guidance
  • Building intuition
  • Additional reference

User guide

• User guide
  • Start here
  • Task guides
  • Declaration model
  • Where to get technical detail

Integration guides

• Integration guides
  • Current examples
  • OpenHCS Example Corpus Map
  • Pipeline compilation workflow
  • Array and memory integration
  • Viewer streaming
  • Fiji streaming
  • OMERO integration
  • Testing guide
  • Choose a guide

API and architecture

• Public API orientation
  • Pipeline declarations
  • CellProfiler import
  • Compilation and execution
  • Primary public types
  • Architecture references
• Architecture quick start
  • Choose the shortest route
  • The public declaration boundary
  • First MCP session
  • CellProfiler pipelines
  • Configuration and processing semantics
  • Unsupported microscope folders
  • Compile before execution
  • Current example authorities
  • Reading map
• Architecture reference
  • Architecture front door
  • Declaration and compilation
  • Runtime
  • Interop and application boundaries
  • Specialized subsystems
  • Documentation status
  • Architecture invariants

Development

• Developer guide
  • Architecture and extension workflows
  • Focused development guides
  • Repository setup and verification
  • Related architecture
• Reference Documentation
  • Experimental Configuration Syntax Reference
  • Configuration References
  • File Format Specifications
  • Example files
  • Quick Reference
• Appendices
  • Glossary

Indices

• Index

• Module Index

• Search Page