Morphological Segmentation help

i am having an issue with my morphological segmentation, i have tried researching months on how to do a smooth segmentation and quantify my objects but to no avail, can you please make some recommendations, especially pertaining to the contours that i am having problems with in my image.

To start @reubensey - it’s best to never use the JPEG file format for saving/processing images for quantitative analysis of any kind. You can read more about why JPEGs are not a good idea - ever (follow the link). So be sure to save/process your images as TIFFs or the proprietary file format provided by your system… and use Bio-Formats to import your images.

But as a quick test… I just ran a quick Gaussian blur (2 pixel radius), Minimum filter (2 pixel radius), and then Variance (2 pixels again)… then running the Morphological Segmentation plugin with MorphoLibJ I got decent segmentation:

Obviously - this can be refined… but gives you a start. This was also under the assumption that you want to segment those lighter-colored blobs.

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thanks for the education and the quick response. I will avoid the Jpeg next time. However, you will realize that, the contours are very challenging as displayed in the image, considering the wonderful results displayed in this piece, “” execution i can say was 100%. that’s what i am trying to achieve best. Nonetheless, thanks. any other information will be very much appreciated. Attached are two images from the link i mentioned.