Workflows


Tutorial about MorphoLibJ: using morphological reconstructions to isolate objects

Fabrice's picture
Workflow Author: 

Fabrice Cordelières

Dependencies: 
Workflow Language: 
Dimension: 
3D
Input data type: 
Any ImageJ compatible input
Comment / Instructions: 

When trying to isolate objects, one strategy might be to use regular morphological operations (opening/closing) to remove small objects that are not of interest. In case small objects are made of a large number of pixels, this operation might impair the remaining objects' contours. Alternative strategy might be to use morphological reconstruction. In short, seed are placed on the image, on objects, then conditionnal dilation is performed from those seeds.

Here is how to proceed, using MorphoLibJ:

  • Open an image
  • Use the multi-point selection tool and place seeds on objects of interest
  • Create a new image of same size, black background
  • Transfer the selection to the new image (Edit/Selection/Restore selection)
  • Draw (make sure you're using white foreground) the multiple point selection
  • Launch the Morphological reconstruction plugin: Plugins/MorphoLibJ/Morphological reconstruction
Rating: 
0
No votes yet