Image Segmentation Scenario¶
Segment a 3D membrane-marker image and measure cell properties
Browsing
Load image p58-t0_imgFus_down_interp_2x.inr.gz
Export to manager
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.
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
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