Reference

Look up exact OpenHCS configuration fields, file formats, and syntax. These pages describe the product as it is; task instructions belong in the how-to guides and background belongs in the concepts section.

• Configuration fields
  • Global configuration
  • Pipeline configuration
  • Step configuration
  • Desktop UI configuration
• Desktop window reference
• Dimensionality and measurement capabilities
  • How dimensionality is declared
  • Current segmentation boundary
  • Current volumetric measurements
  • Measurement families
  • Validation boundary
• Experimental-analysis workbook syntax
  • Workbook structure
  • drug_curve_map rows
  • plate_groups sheet
  • Parser constraints
  • Programmatic boundary
• Current examples
  • Thirty complete imported pipelines
  • Minimal declaration
  • Compilation
  • Typed native presets
  • Loose Opera Phenix neurite outgrowth
  • Master multi-plate lab-meeting showcase
  • CellProfiler import
  • Avoid obsolete examples
• OpenHCS Example Corpus Map
  • CellProfiler Pipeline Corpus
  • CellProfiler To OpenHCS Translation
  • Native OpenHCS Examples
  • Operator Workflow
  • MCP Search Terms
  • Live Data Inspection

Reference pages

• Configuration fields — generated global, pipeline, step, and desktop UI configuration fields.

• Desktop window reference — registered stable desktop windows and their current visual surfaces.

• Dimensionality and measurement capabilities — exact plane-local and volumetric segmentation and measurement boundary.

• Experimental-analysis workbook syntax — Excel experimental-design syntax.

• Current examples — current complete pipeline declarations.

• OpenHCS Example Corpus Map — recipe and example-corpus lookup.

Related terminology

Use Glossary for microscopy, pipeline, source, artifact, and runtime terms shared by these references.