Default Pipeline

Spotlob comes with a predefined pipeline, which has some standard routines built-in. It consists of the following process steps

  1. SimpleReader
  2. GreyscaleConverter
  3. GaussianPreprocess
  4. OtsuThreshold or BinaryThreshold
  5. PostprocessNothing
  6. ContourFinderSimple
  7. FeatureFormFilter
  8. CircleAnalysis or LineAnalysis

The default pipeline can be configured with parameters of returned by the following function

spotlob.defaults.default_pipeline(mode='circle', thresholding='auto')[source]

Gives a pipeline which works for many cases and can be used as a starting point for further tuning or as default for the GUI notebook. By default, features with an area smaller than 500 pixels are ignored.

Parameters:
  • mode (str, optional) –

    this defines the way in which detected features will be evaluated

    • as line the linewidth is calculated
    • as circle an ellipse is fitted and by default features that touch the edge of the image get ignored (the default is “circle”)
  • thresholding (str, optional) –
    • auto uses Otsu’s thresholding algorithm
    • simple uses a fixed threshold value, 100 by default (the default is “auto”)
Returns:

the pipeline including default parameters
Return type:

Pipeline