Visual + Python
Build visually, edit generated Python, and inspect typed artifacts without translating between pipeline formats.
Open-source high-content screening
Microscopy pipelines,
without the black box.
Install OpenHCS 0.6.2 from PyPI and stream results to Napari
or Fiji. This release adds supported CellProfiler
.cppipe import and local MCP access for agents while keeping one
typed execution model from source images to measurements.
pipeline.py
typed · inspectable · portable
SOURCE BINDINGS
Your microscopy data
ImageXpress · Opera Phenix · files
FUNCTION STEP
Correct illumination
group_by · variable components
FUNCTION STEP
Segment & measure
artifacts · CP semantics
ARTIFACTS
Images & measurements
reviewable at every stage
The desktop workspace
See the whole experiment.
Build pipelines, manage plates, inspect images, and follow runtime state from one desktop workspace.
Watch the five-minute demo
OpenHCS desktop · click to watch
One execution model
Visual when you want it.
Visual when you want it.
Python when you need it.
The UI, generated Python, headless runtime, and local MCP surface all use the same pipeline declarations.
Import .cppipe OpenHCS 0.6.2
Lower supported CellProfiler modules into ordinary OpenHCS declarations; unsupported modules fail explicitly.
Napari + Fiji
Stream images and results to either viewer from the same compiled pipeline.
GPU libraries + custom functions
Decorate ordinary Python functions for CuPy, PyTorch, JAX, TensorFlow, or pyclesperanto. They gain contract validation, UI integration, and automatic memory conversion.
openhcs[gpu]
Bio-Formats image I/O OpenHCS 0.6.2
Read microscopy images and dimensional metadata through the Bio-Formats backend.
Bio-Formats
0.6.2
openhcs[bioformats]
Local MCP in OpenHCS 0.6.2
OpenHCS MCP
Give your agent the
same mental model.
The mcp extra and local stdio server ship with OpenHCS
0.6.2. Codex configuration, Claude MCPB sources, and
official registry metadata accompany the release. Production MCPB signing,
directory submissions, and any hosted connector remain separate deployment work.
- 01 Function discovery and typed pipeline authoring over local stdio
- 02 Codex configuration and Claude packaging from the same versioned source
- 03 Explicit read/write roots for microscopy data and outputs
- 04 A separate authenticated UI bridge rather than PyQt inside MCP
OpenHCS 0.6.2 release
Install your way.
Use a desktop installer with no Python setup, or install from PyPI for headless systems and custom environments.
Desktop installers
No Python setup required
GitHub release
Download for WindowsDownload and run — no ZIP to extract
Download for macOSOpen the DMG, then open OpenHCS Installer
User-scoped, CPU-only installation with CellProfiler compatibility, local MCP, Napari, and Fiji/Bio-Formats support; GPU libraries are not included. Fiji Java components are resolved on first use. Initial assets are not code-signed, and the macOS app is not notarized, so your OS may ask you to confirm trust.
Manual, headless, and GPU installs
For existing Python environments
PyPI
$ python -m pip install "openhcs[gui,viz,bioformats,mcp,cellprofiler-compat]"
$ openhcs0.6.2 current releasePython 3.11+Windows · macOS · LinuxMIT licensed