Modifying summary and saving results

Hello !

I am really a beginner, and I have 2 little questions :

  • I run the “analysis particles” and obtain the summary thanks to it. The only problem is that, sometimes, I need to add/remove the particles using the Roi Manager. But this doesn’t change my summary. Is there a way to update the summary ? I tried to recreate the values thanks to the the “measure” button, but the parameters are not the same. And it would be much easier if I could just directly update the summary.

  • When I save the results as .xlsx, I can’t open the file, because apparently it’s a .csv, so I have to save them as .csv and then use some tricks in excel to put the results in different columns and then save as .xlsx . I am sure there is something simple but I am missing it…

Thanks for your help !

Welcome to the forum:

The summary is the output of the Particle Analyzer and that is not really restricted by the ROI Manager and goes only via a binary mask. I played around with Selections and Overlays but it seems to be tricky to do what you want.

The only really “good” way I found was instead of deleting the ROI you could fill the mask with a 0 value to delete that particular particle in the binary mask. You just have to specify black (0,0,0) in the color picker and then press ROI Manager > Fill. Then redo the Particle Analyzer.

But honestly that would be to much pointy-clicky work for me already. I would just measure in the ROIs that are left and then in the downstream data analysis create said summary.

Fiji by default cannot save to a .xls or .xlsx. There is a plugin for this:


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Thank you so much for your answer Christopher !

I will try your trick !

I don’t understand the last part. How could I create the summary in a downstream analysis? My problem is that when I click on “measure” by myself, I don’t have the same info than in the summary.

Thanks for the plugin !


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Ahh you mean the individual measurements. Sure you can get them.
The Summary provides you with the following measurements:

Count, Total Area, Average Size, % Area, Mean, Circularity, Solidity.

Which are just the:

Count - sum of all ROIs, as in count the number of rows
Total Area - sum of the Area measurement
Average Size - mean of the Area measurement
% Area - Area of Image / Total Area * 100
Mean - average of the mean gray value per ROI
Circ. - average of the circularity measurement per ROI
Solidity - average of the solidity measurement per ROI

Just activate the corresponding measurements under to get the measurements per ROI. For Circularity and Solidity you need to activate the Shape descriptors.
Analyze > Set Measurements …




just some small additions to what @schmiedc already answered:

  1. Constructing your own summary from the measurements seems indeed easiest. Note that you can run the same measurements as ParticleAnalyzer directly from the ROI Manager (so it uses Roi’s as input instead of a binary image). This could be convenient if you interact with/add/delete Roi’s and then want to measure again. Select the Roi’s in the manager that you want to measure (or deselect all, then it will measure all). Then click on “Measure”

You could also hijack the “Multi-measure” tool (Roi manager > More >Multi-measure). This tool can clear the result table before adding the new measurements. It can also handle measurements in multiple slices but that it probably irrelevant for you.

  1. Opening a csv file in Excel is possible and pretty straightforward. Open excel and click:
    File > Import >csv . Then choose your file. Make sure that the deliminator is set correctly to “comma”.
    (This is the menu path on MacOS but I imagine the Windows path is quite similar)
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