Cell Counter, Load Markers, ImageJ freezes



I have been using the plugin "Cell counter" and am running into major problems.

After I reopen the original image, I launch the Cell Counter plugin but when I try to load the cell marker xml file saved from a previous session using the "Load Markers" function, ImageJ completely freezes. I have to force quit with Windows Task Manager in order to do anything else. 

I have made sure that the image filename embedded in the xml file is the exact same name as the original image that I opened first. What is weird that this doesn't happen in all cases. Sometimes the load marker button works fine to load saved markers. I have opened the cell counter files in Notepad to compare what is different between the ones that load properly and those that do not, and I have no clue what the difference is!!

Please help! I have upwards of 9 hours of quantification that I cannot access and am dreading the possibility of having to re-do all these counts


Just in case you haven’t checked, are you using an up-to-date version of Fiji with Cell Counter built in, or some other setup? Do you have the same problem on other computers, or after re-installing ImageJ/Fiji?

In the worst case you might be able to retrieve the info from the XML file as suggested here.

Hope this helps.


This suggestion alone won’t save your 9 hours of effort, but: the Cell Counter plugin is ancient and its functionality has nearly all been rolled into core ImageJ. Have you considered using the built-in multi-point tool? You can save and load the multi-points using the ROI Manager:

  • Press T to add the multi-point selection to the ROI Manager.
  • Press the More » button, then choose Save....
  • Load it again later via Open... in that same More » menu.

As for your already-measured points, as @tswayne suggests, you could parse the XML file yourself and convert it. If you need help, post a link here to your XML file, and maybe someone has time to do the conversion for you to the ROI format. I might even create a reusable tool for that, since this has come up more than once. :smile: