Viewer

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.

Viewer

• 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.