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.
- 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
zcoordinate. For the type
pngseq, the slider value corresponds to the png filename e.g. slider value 25 shows the file
- Multiple segmentations can be selected at the same time.
- 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.
- create a segmentation for currently selected dataset, given model and new segmentation name
- create a new model from an existing model, given annotation and new model name. Epochs determines the amount of fine-tuning.