Image: Raw image to be processed with a neural network.
Model filter: Choose to only show models tagged with `plantseg`.
PlantSeg model: Select a pretrained PlantSeg model. Current model description: Unet trained on confocal images of Arabidopsis Ovules on 1/2-resolution in XY with BCEDiceLoss.
BioImage.IO model: Select a model from BioImage.IO model zoo.
None
Mode: Select the mode to run the prediction.
Image: Raw image to be processed with a neural network.
Model filter: Choose to only show models tagged with `plantseg`.
BioImage.IO model: Select a model from BioImage.IO model zoo.
Widget: Watershed - Generate Superpixels
None
Boundary image: Raw boundary image or boundary prediction to use as input for Watershed.
Mode: Define if the Watershed will run slice by slice (faster) or on the full volume (slower).
Boundary threshold: A low value will increase over-segmentation tendency and a large value increase under-segmentation tendency.
Minimum segment size: Minimum segment size allowed in voxels.
Show advanced parameters: Show advanced parameters for the Watershed algorithm.
Widget: Agglomeration - Merge Superpixels into Instances
None
Boundary image: Raw boundary image or boundary prediction to use as input for clustering.
Nuclei foreground: Nuclei foreground prediction or segmentation.
Over-segmentation: Over-segmentation labels layer (superpixels) to use as input for clustering.
Agglomeration mode: Select which agglomeration algorithm to use.
Under/Over segmentation factor: A low value will increase under-segmentation tendency and a large value increase over-segmentation tendency.
Minimum segment size: Minimum segment size allowed in voxels.
