Configuration Reference#

PhenoTypic’s behavior can be configured through the phenotypic.settings_ module. Import settings before other PhenoTypic modules when modifying them.

import phenotypic.settings_
# Modify settings here, before importing other modules

Global Settings#

Settings are accessed via the phenotypic.settings_ module. Key configuration options include:

Image Defaults

  • default_bit_depth — Default bit depth for new images (8 or 16)

  • default_gamma — Default gamma encoding (GAMMA_ENCODINGS.SRGB)

  • default_illuminant — Default illuminant ("D65")

Processing

  • detect_mode — Default detection matrix source channel ("gray")

  • n_jobs — Default parallelism for batch operations

Visualization

  • plotly_template — Default Plotly template for .dash() figures

  • matplotlib_backend — Matplotlib backend selection

Constants#

Key constants are available in phenotypic.tools_.constants_:

from phenotypic.tools_.constants_ import GAMMA_ENCODINGS, METADATA

GAMMA_ENCODINGS.SRGB     # Standard sRGB gamma encoding
GAMMA_ENCODINGS.LINEAR   # Linear RGB (no gamma)

Pipeline JSON Format#

Pipeline configurations are stored as JSON with the following structure:

{
  "phenotypic_version": "0.x.y",
  "name": "pipeline_name",
  "description": "...",
  "ops": [
    {
      "class": "GaussianBlur",
      "module": "phenotypic.enhance",
      "params": {"sigma": 2.0, "mode": "reflect"}
    }
  ],
  "meas": [
    {
      "class": "MeasureSize",
      "module": "phenotypic.measure",
      "params": {}
    }
  ]
}

All operation classes and their parameters are captured. The PhenoTypic version is recorded to warn about compatibility issues when loading pipelines saved with a different version.