Here is what worked for me for the above image:
1) Crop the scale bar.
2) Remove the shadow gradient.
3) Simple thresholding based on histogram.
4) Remove any connected components smaller than 100 Pixels.
5) Imfill the holes, including the regions that are bounded by the image borders. (Create a routine that adds a line of 1s outside the borders, 1 border at a time, then fill.)
6) Close the image with a 1 radius disk.
This I did in 2 minutes, no more time to improve on this, but I think you can take it from there, below is what it looks like at step 6. You can alter the parameters at different steps if you want each bubble to look as seperate as possible etc.
