Problems with watershedding (deprecated version) about imglib2-algorithm HOT 3 CLOSED

Can you post a self-contained example somewhere, including the images?

from imglib2-algorithm.

Hi tpietzsch,

I have put up all the methods and the image needed in one class here:
https://github.com/PreibischLab/ImgLib2TestEnvironment/tree/master/src/main/java/varun
The class of interest is watershedding.java on this page.

The image used is in src/main/resources/. To prep the image for watershedding, distance transform in performed and then intensity inverted DT-image is used to calculate local maxima to get the seed image for the watershedding part, the watershedding method is the first method in the class. I have cherry picked all the methods needed for the watershedding part so the program looks like a JUnit test but for a self contained example I thought it would help identify the error in my implementation (in the method OldWatersherImage there).

Hope this helps. Thanks.

from imglib2-algorithm.

You should set the Watershed parameters before you call process()
https://github.com/PreibischLab/ImgLib2TestEnvironment/blob/master/src/main/java/varun/Watershedding.java#L79-L84

You should label each seeds differently. In your case you label them all 1. Therefore the whole image ends up labeled as 1, as you can verify using

ImageJFunctions.show( outputLabeling.getStorageImg() ).setTitle( "labeling storage image" );

Your code for extracting the "Watershed Images" doesn't work, because
https://github.com/PreibischLab/ImgLib2TestEnvironment/blob/master/src/main/java/varun/Watershedding.java#L105
you are not reading the labeling image but the (empty) output image.

I'm closing this issue. The problem is clearly with your code, not with the imglib2 watershed implementation.

from imglib2-algorithm.