Suggestions on How to segment this


Hi, I am looking for suggestions about what tools might work best for this problem. I am trying to quantify as a percentage area covered the amount of tissue occupied by the lipid based vaculoles (While circular objects) in this image that are not the lumen (Inside hole) of the tubules represented.

I think my approach should be to isolate (Segment) the tissue area, for instance not all of my Images will be entirely tissue see upper left corner for example. then segment out the vacuoles but I’m not finding tools that preform this well.

Does anyone have suggestion regarding good tools or a better approach?



Perhaps you can better describe or at least annotate what regions you need to segment? It’s not clear to me at least… We are all coming from different scientific backgrounds - so cannot necessarily follow your descriptions.

To help get you started though - here are a few helpful links/tools for ImageJ and Segmentation within ImageJ:



Also for this kind of images, you should try:

Both of them are open source tools targeting primarily histology images.


Check this youtube out.