openhcs 0.5.13

High-Content Screening image processing engine with native GPU support

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      |_|           High-Content Screening

Bioimage analysis platform for high-content screening
Compile-time validation · Bidirectional GUI↔Code · Multi-GPU · LLM pipeline generation · 574+ functions

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OpenHCS processes large microscopy datasets (100GB+) with a compile-then-execute architecture. Pipelines are validated across all wells before any processing starts, preventing failures after hours of computation. Design pipelines in the GUI, export to Python, edit as code, and re-import — switching seamlessly 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["5-Phase Compiler<br/>(validate)"]
        EX["Multi-Process Executor<br/>(1 process/well · multi-GPU)"]
        FN["574+ Unified 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

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⚡ Key Capabilities

🛡️ Compile-Time Validation Pipelines are compiled through 5 phases before execution — path planning, store declaration, materialization flags, memory contract validation, GPU assignment — then frozen into immutable contexts. 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 1 process per well via ProcessPoolExecutor with GPU scheduler assigning devices to workers. CUDA spawn-safe. Scales from laptops to multi-GPU workstations — process 100GB+ datasets with OME-ZARR compression (LZ4, ZSTD, Blosc).
🔌 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 @special_outputs declaratively routes analysis results to CSV, JSON, ROI ZIP (ImageJ-compatible), or TIFF stacks via pluggable format writers. ROIs stream to Fiji/ImageJ. Results appear alongside processed images with no manual I/O code.
🔬 Process-Isolated Napari & Fiji Stream images to Napari and Fiji/ImageJ in real-time during pipeline execution. Viewers run in separate processes via ZeroMQ — no Qt threading conflicts. Persistent viewers survive pipeline completion. PolyStore treats viewers as streaming backends.	🪟 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.

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🧩 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 & streaming	Pluggable backends for storage (disk, memory, ZARR) and streaming (Napari, Fiji) — viewers are just backends. Virtual workspace, atomic writes, format detection, ROI extraction
ZMQRuntime	Distributed execution	ZMQ client-server for remote pipeline execution, progress streaming, and OMERO server-side processing
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

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🔬 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.

574+ 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

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🚀 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]

# Launch the application
openhcs

# Or use programmatically — real pipeline from a neuroscience experiment
from openhcs.core.orchestrator.orchestrator import PipelineOrchestrator
from openhcs.core.steps.function_step import FunctionStep
from openhcs.constants.constants import VariableComponents
from openhcs.processing.backends.processors.cupy_processor import (
    stack_percentile_normalize, tophat, create_composite
)
from openhcs.processing.backends.pos_gen.ashlar_main_gpu import ashlar_compute_tile_positions_gpu
from openhcs.processing.backends.assemblers.assemble_stack_cupy import assemble_stack_cupy
from openhcs.processing.backends.analysis.cell_counting_cpu import count_cells_single_channel

steps = [
    FunctionStep(func=[
        (stack_percentile_normalize, {'low_percentile': 1.0, 'high_percentile': 99.0}),
        (tophat, {'selem_radius': 50, 'downsample_factor': 4})
    ], name="preprocess", variable_components=[VariableComponents.SITE]),

    FunctionStep(func=[create_composite],
                 name="composite", variable_components=[VariableComponents.CHANNEL]),

    FunctionStep(func=[ashlar_compute_tile_positions_gpu],
                 name="find_positions", variable_components=[VariableComponents.SITE]),

    FunctionStep(func=[(assemble_stack_cupy, {'blend_method': 'fixed'})],
                 name="assemble", variable_components=[VariableComponents.SITE],
                 force_disk_output=True),

    FunctionStep(func=[count_cells_single_channel],
                 name="count_cells", variable_components=[VariableComponents.SITE]),
]

orchestrator = PipelineOrchestrator("path/to/plate")
orchestrator.initialize()
compiled = orchestrator.compile_pipelines(steps)  # Validates everything first
orchestrator.execute_compiled_plate(steps, compiled, max_workers=5)

📦 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)

GPU requires CUDA 12.x. For CPU-only: OPENHCS_CPU_ONLY=true pip install openhcs[gui]

🗄️ OMERO integration

OMERO requires zeroc-ice (not on PyPI). The custom setup.py installs it automatically:

pip install 'openhcs[omero]'     # Auto-installs zeroc-ice

If that fails, alternatives:

python scripts/install_omero_deps.py   # Standalone script
pip install -r requirements-omero.txt  # Requirements file

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

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📖 Documentation

📘 Read the Docs	Full API docs, tutorials, guides
📊 Coverage Reports	Test coverage analysis
🏗️ Architecture	Pipeline system · GPU management · VFS · Config framework
🎓 Getting Started	Installation · First pipeline

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⚙️ Architecture Highlights

5-Phase Pipeline Compilation — catch errors before execution starts

Define → Compile → Freeze → Execute
         ├─ 1. Path planning
         ├─ 2. ZARR store declaration
         ├─ 3. Materialization flags
         ├─ 4. Memory contract validation
         └─ 5. GPU assignment
              → context.freeze()  # immutable

Pipelines are compiled for every well before any processing begins. Frozen contexts prevent state mutation during execution. 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 — PolyStore streaming, function discovery, memory types

• PolyStore Unified I/O: Storage backends (disk, memory, ZARR) and streaming backends (Napari, Fiji) behind one API — viewers are just backends. Virtual workspace path translation, atomic writes, ROI extraction.
• Automatic Function Discovery: 574+ 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 →

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🤝 Contributing

git clone https://github.com/OpenHCSDev/OpenHCS.git && cd OpenHCS
pip install -e ".[all,dev]"
pytest tests/

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

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📄 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).