Voronoi Segmentation

Performs a Voronoi based segmentation of images. Requires an input table with a source image and a labeling of the corresponding seed regions.

Options

Image to work on

Select the column that contains the full image of the cells.

Seed regions image

Select the column that contains image with the seed regions.

Background threshold value

If a pixel value is less than this value it is considered being background and is not part of any cell.

Fill holes

Fills holes within segments of the same label in a post-processing step.

Result column

Appends either a column with the complete voronoi based segmentation, the voronoi segmentation without the seeds or both.

Dimension selection

This component allows the selection of dimensions of interest. If an algorithm cannot, as it only supports fewer dimensions than the number of dimensions of the image, or shouldnot, as one wants to run the algorithm only on subsets of the image, be applied on the complete image, the dimension selection can be used to define the plane/cube/hypercube on which the algorithm is applied. Example 1 with three dimensional Image (X,Y,Time): An algorithm cannot be applied to the complete image, as it only supports two dimensional images. If you select e.g. X,Y then the algorithm will be applied to all X,Y planes individually. Example 2 with three dimensional Image (X,Y,Time): The algorithm can be applied in two, three or even more dimensions. Select the dimensions to define your plane/cube/hypercube on which the algorithm will be applied.

Views

Table Cell View

Alternative view on the result images and segmentation.

Workflows

• 01_TrackmateKNIME Hub
• 06_High_Content_ScreeningKNIME Hub
• 12_3D_SegmentationKNIME Hub
• 19_Slice_LoopKNIME Hub
• 20200405IdentifyNuclei_measure2ChannelsKNIME Hub
• Show all 14 workflows

Links

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Developers