Image Segmentation Scenario

Segment a 3D membrane-marker image and measure cell properties

  1. Browsing

    • Load image p58-t0_imgFus_down_interp_2x.inr.gz

    • Export to manager

  2. Segmentation

    • Drop the image from the manager it it has not been done automatically

    • Choose the plugin seededWatershedSegmentation

    • Set the following parameter values:

      • h_min -> 2

      • volume_threshold -> ~1000

    • Press Apply

Once the computation is finished, the output visualization will show the result. Switch the view to 2D (-> sync) and slider to compare the input and output.

  1. Cell Image Quantification

    • Choose the plugin cellFeaturesTissueImage

    • Select the features volume and layer in the list

    • Press Apply

In the view menu of the 3D viewer, switch the visualization plugin to …MarchingCubes and display the property layer

  1. Pipeline

    • Open the pipeline panel at the bottom

    • Edit the pipeline name and information

    • Press on the save icon to export the pipeline as a JSON file

Video