openhcs

OpenHCS

Bioimage analysis platform for high-content screening
Compile-time validation · Bidirectional GUI↔Code · Multi-GPU · LLM pipeline generation · Extensible function registry

🎬 Demo

Watch demo in browser player: https://openhcs.readthedocs.io/en/latest/_static/openhcs.mp4
Mirror link (GitHub raw): https://raw.githubusercontent.com/OpenHCSDev/OpenHCS/refs/heads/main/docs/source/_static/openhcs.mp4

OpenHCS processes large microscopy datasets with a compile-then-execute architecture. Pipelines are validated across the selected execution axes before processing starts, preventing late failures after expensive work. Design pipelines in the GUI, export to Python, edit as code, and re-import — switching between visual and programmatic workflows.

graph LR
    subgraph Microscopes
        IX[ImageXpress]
        OP[Opera Phenix]
        OM[OMERO]
    end

    subgraph OpenHCS Platform
        PD["Pipeline Designer<br/>(GUI ⇄ Code ⇄ LLM)"]
        CO["Typed Compiler<br/>(resolve + validate)"]
        EX["Multi-Process Executor<br/>(1 process/well · multi-GPU)"]
        FN["Registry-Discovered Functions<br/>scikit-image · CuPy · pyclesperanto<br/>PyTorch · JAX · TF · CuCIM · custom"]
        PS["PolyStore<br/>(Memory ↔ Disk ↔ ZARR ↔ Stream)"]
    end

    subgraph Viewers
        NA[Napari]
        FJ[Fiji/ImageJ]
    end

    IX --> PD
    OP --> PD
    OM --> PD
    PD --> CO --> EX
    EX --> FN --> PS
    PS --> NA
    PS --> FJ

⚡ Key Capabilities

🛡️ Compile-Time Validation Configuration is resolved once into step snapshots and a compilation session. Typed plans then validate sources, artifacts, materialization, memory contracts, and worker requirements before execution begins. Errors surface immediately, not after hours of processing.	🔄 Bidirectional GUI ↔ Code Design pipelines visually, export as executable Python, edit in your IDE, re-import to the GUI. Code generation works at any scope level — function patterns, individual steps, pipeline configs, full orchestrator scripts — any window holding objects can generate and re-import code.
🧠 LLM Pipeline Generation Describe a pipeline in natural language and get executable code. Built-in chat panel with local Ollama or remote LLM endpoints. Dynamic system prompts built from the actual function registry — the LLM knows every available function and its signature.	⚡ Full Multiprocessing & Multi-GPU Bounded worker lanes use ProcessPoolExecutor by default, with deterministic well assignment and sequential processing inside each lane. A GPU scheduler assigns devices to workers; single-worker and debugging configurations can use inline or threaded execution.
🔌 Any Python Function Register any Python function by decorating it with @numpy, @cupy, @pyclesperanto, @torch, or other memory type decorators. Custom functions get automatic contract validation, UI integration, and appear alongside built-in functions. Persisted to ~/.openhcs/custom_functions/.	📊 Results Materialization Callable and module artifact contracts declare semantic outputs independently of Python argument names. The artifact graph and materialization plans route images, measurements, object labels, relationships, tables, and files to their configured stores and exporters.
🔬 Process-Isolated Napari & Fiji Stream images to Napari and Fiji/ImageJ in real time during pipeline execution. OpenHCS StreamingConfig declarations and viewer adapters own identity, display, and persistence policy. PolyStore builds generic storage and streaming payloads; ZMQRuntime supplies process-isolated transport, readiness, acknowledgments, and lifecycle.	🪟 Live Cross-Window Updates Edit a value in GlobalPipelineConfig — watch it propagate in real-time to PipelineConfig and StepConfig windows. Dual-axis resolution (context hierarchy × class MRO) with scope isolation per orchestrator.
🧬 CellProfiler Pipeline Import Open .cppipe files in the desktop application or lower them from Python into ordinary PipelineConfig and FunctionStep declarations. Named images, objects, measurements, relationships, and exports use the same typed compiler and runtime as native OpenHCS pipelines; compatibility reports and the Official30 corpus keep tested coverage explicit.	🤖 MCP Agent Automation Use the local stdio MCP server with Codex, Claude Desktop, and other clients, or deploy the separately secured hosted HTTP surface. Capability profiles, schemas, knowledge, UI attachment, authoring, execution, runtime inspection, and viewer review are projected from one typed capability registry rather than duplicated tool lists.

🧩 The OpenHCS Ecosystem

OpenHCS is built on 8 purpose-extracted libraries — each solving a general problem, each independently publishable, all woven into a cohesive platform:

graph TD
    OH["OpenHCS Platform<br/>(domain wiring + pipelines)"]

    OH --> OS["ObjectState<br/>(config)"]
    OH --> AB["ArrayBridge<br/>(arrays)"]
    OH --> PS["PolyStore<br/>(I/O + streaming)"]
    OH --> ZR["ZMQRuntime<br/>(exec)"]
    OH --> QR["PyQT-reactive<br/>(forms)"]

    OS --> PI["python-introspect<br/>(signatures)"]
    OH --> MR["metaclass-registry<br/>(plugins)"]
    OH --> PC["pycodify<br/>(serialization)"]

Library	Role in OpenHCS	What It Does
ObjectState	Configuration framework	Lazy dataclasses with dual-axis inheritance (context hierarchy × class MRO) and contextvars-based resolution
ArrayBridge	Memory type conversion	Unified API across NumPy, CuPy, PyTorch, JAX, TensorFlow, pyclesperanto with DLPack zero-copy transfers
PolyStore	Unified I/O & stream payloads	Generic storage and streaming payload primitives, backend lifecycle, virtual workspaces, atomic writes, format detection, and ROI extraction
ZMQRuntime	Process & transport runtime	Generic request, status, progress, cancellation, process-lifecycle, and viewer-control transport protocols
PyQT-reactive	UI form generation	React-style reactive forms from dataclasses with cross-window sync and flash animations
pycodify	Code ↔ object conversion	Python source as serialization format — type-preserving, diffable, editable, with collision handling
python-introspect	Signature analysis	Pure-Python function/dataclass introspection for automatic UI generation and contract analysis
metaclass-registry	Plugin discovery	Zero-boilerplate registry system powering microscope handler and storage backend auto-discovery

🔬 Microscope & Function Support

Microscope Systems System Vendor ImageXpress Molecular Devices Opera Phenix PerkinElmer OMERO Open Microscopy OpenHCS Format Native Auto-detected. Extensible via metaclass-registry.

Functions — Automatic Discovery Library Functions Acceleration pyclesperanto 230+ OpenCL GPU CuCIM/CuPy 124+ CUDA GPU scikit-image 110+ CPU PyTorch / JAX / TF ✓ CUDA GPU OpenHCS native ✓ Mixed Unified contracts, automatic memory conversion via ArrayBridge.

Processing domains: image preprocessing · segmentation · cell counting · stitching (MIST + Ashlar GPU) · neurite tracing · morphology · measurements

🚀 Quick Start

# Basic installation with GUI
pip install openhcs[gui]

# Add Napari viewer
pip install openhcs[gui,napari]

# Add Fiji/ImageJ viewer
pip install openhcs[gui,fiji]

# Add both viewers
pip install openhcs[gui,viz]

# Add GPU acceleration (CUDA 12.x required)
pip install openhcs[gui,gpu]

# Full installation (GUI + viewers + GPU)
pip install openhcs[gui,viz,gpu]

# Add the local MCP server for agent clients
pip install openhcs[gui,mcp,viz]

# Launch the application
openhcs

# Launch the local MCP server over stdio
openhcs-mcp

# Or lower a CellProfiler pipeline into public OpenHCS declarations
from pathlib import Path

from objectstate import ensure_global_config_context
from openhcs.core.config import GlobalPipelineConfig
from openhcs.core.orchestrator.orchestrator import PipelineOrchestrator
from openhcs.interop.cellprofiler.pipeline_import import import_cellprofiler_pipeline

plate_path = Path("/data/plate").resolve()
ensure_global_config_context(GlobalPipelineConfig, GlobalPipelineConfig())
steps, pipeline_config = import_cellprofiler_pipeline(
    "analysis.cppipe",
    source_root=plate_path,
)

orchestrator = PipelineOrchestrator(
    plate_path,
    pipeline_config=pipeline_config,
).initialize()
compilation = orchestrator.compile_pipelines(steps)
execution_bundle = compilation["execution_bundle"]

The GUI and execution services consume the same list[FunctionStep], PipelineConfig, and typed execution bundle. See the API orientation for the explicit low-level execution call and progress lifecycle.

📦 All installation options

pip install openhcs              # Headless (servers, CI)
pip install openhcs[gui]         # Desktop GUI
pip install openhcs[gui,napari]  # GUI + Napari viewer
pip install openhcs[gui,viz]     # GUI + Napari + Fiji
pip install openhcs[gui,viz,gpu] # Full installation
pip install openhcs[gpu]         # Headless + GPU
pip install openhcs[omero]       # OMERO integration
pip install -e ".[all,dev]"      # Development (all features)

The gpu extra requires a compatible CUDA 12 environment. For a CPU-only desktop installation, install openhcs[gui] without the gpu extra.

🗄️ OMERO integration

OMERO requires zeroc-ice, whose compatible wheels are not published through the normal project metadata. Install the helper requirements before the extra:

python scripts/install_omero_deps.py
pip install 'openhcs[omero]'

Equivalent requirements-file installation:

pip install -r requirements-omero.txt
pip install 'openhcs[omero]'

Supported on Python 3.11 and 3.12. See Glencoe Software for manual installation.

📖 Documentation

📘 Read the Docs	Full API docs, tutorials, guides
🏗️ Architecture	Typed compiler · sources · artifacts · runtime values · package boundaries
🎓 Getting Started	Installation · First pipeline

⚙️ Architecture Highlights

Resolved, typed pipeline compilation — catch errors before execution starts

PipelineConfig + list[FunctionStep]
        ↓ resolve once
StepSnapshot + CompilationSession
        ↓ derive and validate
typed CompiledStepPlan objects
        ↓ package
CompiledExecutionBundle
        ↓ execute
runtime values + materialized artifacts

The authoring surface remains an ordered linear step list. ObjectState inheritance keeps defaulted configuration sparse, while compilation derives and exposes the exact source and artifact dependencies required for execution; the derived dependency graph is not a second workflow the user must author.

Pipelines are compiled for every selected execution axis before processing begins. Runtime workers consume the compiled bundle rather than reinterpreting mutable declaration objects. Read more →

Dual-Axis Configuration — context hierarchy × class MRO

Resolution walks two axes simultaneously: the context stack (Global → Pipeline → Step) and the class MRO (inheritance chain). Built on contextvars for thread-safe, scope-isolated resolution. Preserves None vs concrete value distinction for proper field-level inheritance. Powered by ObjectState. Read more →

Bidirectional GUI ↔ Code — code generation at any scope level

Any window holding ObjectState objects can generate and re-import executable Python:

Function patterns · Individual steps · Pipeline configs · Full orchestrator scripts
              ↕  generate / AST-parse back  ↕

Each scope encapsulates all lower-scope imports. Generated code is fully executable without additional setup. Edit in your IDE or external editor, save, and the GUI re-imports via AST parsing. Powered by pycodify + python-introspect. Read more →

Cross-Window Live Updates — class-level registry + Qt signals

A class-level registry tracks all active form managers. When a value changes in any config window, Qt signals propagate the change to every affected window with debounced, scope-isolated refreshes. Global → Pipeline → Step cascading with per-orchestrator isolation. Powered by PyQT-reactive. Read more →

More patterns — storage, viewer integration, function discovery, memory types

• Storage and viewer streaming: PolyStore owns generic storage and streaming payload primitives; ZMQRuntime owns process, transport, readiness, acknowledgment, and lifecycle protocols; OpenHCS StreamingConfig declarations plus the Napari/Fiji adapters own viewer identity, display, and application policy.
• Automatic Function Discovery: registry-discovered functions with contract analysis and type-safe integration via python-introspect + metaclass-registry
• Memory Type Management: Compile-time validation of array type compatibility with zero-copy conversion via ArrayBridge
• Custom Function Registration: Any Python function decorated with @numpy, @cupy, @pyclesperanto, etc. is auto-integrated with contracts, UI forms, and the function registry
• Evolution-Proof UI: Type-based form generation from Python annotations — adapts automatically when signatures change

Full architecture docs →

🤝 Contributing

git clone --recurse-submodules https://github.com/OpenHCSDev/OpenHCS.git
cd OpenHCS
# Install the eight local packages as described in docs/development_setup.md,
# then install OpenHCS itself:
python -m pip install -e ".[dev,gui]"
OPENHCS_CPU_ONLY=1 python -m pytest tests/unit

Contribution areas: microscope formats · processing functions · GPU backends · documentation

📄 License

MIT — see LICENSE.

🙏 Acknowledgments

OpenHCS evolved from EZStitcher and builds on Ashlar (stitching), MIST (phase correlation), pyclesperanto (GPU image processing), and scikit-image (image analysis).

OpenHCS's CellProfiler interoperability and parity validation build on the CellProfiler project's open-source software, documentation, and public example, tutorial, and benchmark materials. We thank the CellProfiler authors and contributors and the authors of the biological datasets they distribute. Please cite CellProfiler following its official citation guidance, including Stirling et al., CellProfiler 4: improvements in speed, utility and usability (2021). OpenHCS is an independent project and is not endorsed by the CellProfiler project or the Broad Institute.