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Pixel-based Machine Learning for ImageJ and beyond

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imagej-pixml

Playground for Pixel-based Machine Learning for ImageJ and beyond

Blockers:

  • overlay issue - overlays in BDV, overlays in ImageJ2, unification of overlays (ROIs), Overlays need labels (can be potentially turned into RandomAccressibleInterval<LabelingType<..>>), OverlayManager
  • BDV as ImageJ2 DisplayPlugin (and related stuff), that supports the rendering of RandomAccessibleIntervals of different types (e.g. RealType, LabelingType etc. - ColorTable), Overlays, ...

TODOs:

  • Cluster-interface
  • Model/Classifier Display/Manager (to load/save/display models)
  • ...

Commands:

  • Classify & Predict
  • Classify (returns a Model, e.g. to be saved somewhere)
  • Predict (requires a Model)
  • Cluster
  • Model Manager

Use Cases:

Feature Calculation + Build Model + (Optional) Predict

  • input: image and labeling
  • calculate features of the input image
  • build model based on the given feature image and labels
  • prediction of the same input images

Feature Calculation + Prediction

  • input: (multiple) images + model (classifier, e.g. selected from a list of available models)
  • calculate features
  • prediction using the given model (needs to comply with the given features -> model must contain a specification of the features!!!)
  • advantage: model can be reused each for batch-processing

Prediction only

  • input: feature image + model
  • prediction using the given model and features

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