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The viewer is an interface implemented using Dash. It can be used for basic visualizations of BioSegment data. The viewer also allows for annotating, running a segmentation job and fine-tuning a model.

  • Open a dataset via the Dashboard or go to the URL directly e.g. http://localhost/dash/viewer.
  • Use the refresh buttons to update the dropdowns with backend data.

The viewer has 4 components.


  • Given a dataset, segmentations and slider location, a view of a slice of the dataset will be shown. Differently annotated regions will be colored.
  • the slider is the z coordinate. For the type pngseq, the slider value corresponds to the png filename e.g. slider value 25 shows the file 0025.png.
  • Multiple segmentations can be selected at the same time.

Annotations tools

  • classes of interest
    • e.g. mitochondria, ER
    • determined by dataset
  • Stroke width of the annotation brush
  • Selected annotation
  • Create a new annotation for given name
    • when no annotation is selected, will create an empty annotation
    • when an annotation is selected, will copy the annotation and give it the new name.
  • Start editing current annotation
    • The viewer will update with annotation tools
    • when done, click on the done button to save the annotation. Only then will the annotation be saved in the backend.

Run segmentation

  • create a segmentation for currently selected dataset, given model and new segmentation name

Fine-tune model

  • create a new model from an existing model, given annotation and new model name. Epochs determines the amount of fine-tuning.