How to import cell counter files in updated ImageJ


I performed some cell counts using the Cell Counter plugin (Plugin > Analyze > Cell Counter). I gather this has been replaced by the Multi-point tool in the latest version of ImageJ. I had previously saved the dots used to mark counted cells - the default file type for this is a .xml file. I can’t figure out how to open this file and add the markers to my image in the new version now that Cell Counter is not available. The Multi-point tool seems to want a .roi file for this but change .xml to .roi doesn’t work. Any suggestions would be great. I really need to be able to see where the markers were on these images so that I can continue / collect new data without having to start over.


Dear @Liz_Glover,

Where exactly did you get that information? I couldn’t find anything on the plugin’s website.

In general, I don’t think that the new counting functionality of the multi-point tool was intended to replace that plugin and be able to read its outputs.


@stelfrich, in posts such as this and this, the Cell Counter is described as old (not significantly changed since 2010) and buggy, and use of the Multi-Point tool is encouraged as an alternative.

True, you can’t open Cell Counter files, and you can’t name your categories, but in other respects the Multi-Point tool is easier to use and takes advantage of modern ImageJ features like overlays and the ROI manager.

That said, @Liz_Glover, I do still see Cell Counter in my copy of Fiji, but if it’s not in your installation, you should still be able to find a similar version in the Cookbook update site, or install the source files from Github or possibly from here (pre-Fiji version).

For converting existing Cell Counter XML files to ROIs, @ctrueden suggested some ideas here.

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