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I have had problems loading markers too and finally figured out the solution. When you first save the markers on ImageJ it embeds the name of the picture file into the counter file. However, if you try to change the name of either the counter file or the image file later (just renaming the file), even though they appear to match, what is embedded is not changed just by changing the file name. The way to fix this is to open the counter file with a text editor, like notepad or textedit on mac and change the file name so that it matches exactly. Just do markers on a new image and open those marker files with text edit to compare. You will likely see that the embedded file name of the one that is not working is different from what the file is named on your computer when you see the file in finder. Bottom line, when you first save the markers the xml file name you will see is "Cell Counter_picture file name.xml" but if you ever change it or change the picture file name they will not match.
Another thing I found out is that the counter counter will not load markers if there is a # symbol in the picture file name. Make sure you don't have number symbols because it will not recognize this and it will seem as if it is loading (the error message won't pop up) but the markers will not load.
Most likely one or both of these reasons are the cause of your problem. Hope this helps!
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