Once you have your thresholded, binary image run a despeckle to get rid of the small stuff (Process->Noise->Despeckle), then you can either dilate the objects to expand what's left and hopefully it will close the gaps (Process->Binary->Dilate) or you can actually try to close the holes (Process->Binary->Fill Holes). Then run the analyze particles routine.

you can try to analyse your images with ICY (icy.bioimageanalysis.org) segment the images using the HK-Means plug-in which can filter the output by sizes, therefore you can put the minimum and maximum sizes (per pixel). the output with be your ROIs which you can count or do further analysis. also you can try ilastik.org if you have more confluent images, they have easy to follow tutorials on youtube

I usually

1. make a copy of the image, then apply a median filter (Process, Filter: 2 pixels usually works for me) to slightly blur the image for thresholding.

2. Do automatic thresholding on the filtered image to generate binary.

3. Use Analyze Particles to find all the ROIs on the thresholded image. You can exlude small things and non-cicular objects with size and circularity thresholds here. Click "Add to Manager" to send all the ROIs to the ROI Manager.

4. Once you have all the ROIs in the manager, place them onto the original image by selecting it and toggeling "Show All" in the ROI manager.

5. Select "Measure" in the ROI manager. All measurements you have selected in Set Measurements will come up for those ROIs.

Thank you all so much! I actually figured out I was thresholding in the wrong way, but I added all the above advice because it improves the quality of my pictures. Now I have another problem...very very trivial: I can't manage to 1) create a break in my macro such that I run bits of the macro at a time (it only makes me run the whole macro at once); 2) create a shortcut to run my macro by pressing keys, I tried the Plugings>Shortcuts>Create Shortcut but I can't find my macro in the Command line, even after installing the macro. Any advice?