Hi Lukas,

I've attached a plugin you could try - it is intended to let you take any labeled image, and replace the labeled pixels with the corresponding measurement in the results table (whatever that may be).  Note that it is only able to 'see' the Results Table with the exact name 'Results', therefore if you use the 3D Objects Counter you will first need to go to Analyze -> 3D OC Options and ensure the following options are NOT selected:

- 'Show numbers'

- 'Store results within a table named after the image'

You should be able to drag the .java file onto Fiji and run it directly from the script editor.

It was written quickly and so it would be amazing if I haven't made mistakes somewhere... so if you plan to use it for anything please be on the look out for errors.  There may well be plugins out there that already do this, but I couldn't think of any.

Best wishes,

Pete

Hi Peter, thanks for your reply and the file.

It didn't worked perfectly and showed other structures then the original file, but during I've tested your script I mentioned that when I do not use the function "show numbers" I can create a maximum projection with the right colors.

Hi Lukas,

I don't understand what you mean that it didn't work perfectly - is there an error that requires fixing?

I wrote that you should turn off 'show numbers' because the numbers created by the 3D Objects Counter actually involve changing the pixel values in the image (e.g. to become 255) in the places where the numbers are drawn, and these number pixels then do not correspond to real object labels - and there is no way to know completely for sure what the original pixel values should have been.  Since my plugin reads every non-zero pixel as a label, it gives a warning in such cases to draw attention to this fact that it found non-object pixels (better to warn than to ignore).  Are these the 'other structures' you refer to?

In any case, I would only expect the plugin to work without warnings if 'show numbers' was turned off when the Objects Counter was run.

Hi Peter,

as you discribed I didn't use the "show numbers". For the calculation I've choosed the Voxels out of the Result file.

I've linked two exemplary pictures. "Object maps" is the maximum projection of the result of the Object counter, "objects maps make measurement" is the resulted file after using your macro.

Hi Lukas,

I think that looks like it has worked, or is it different from what you expect to see?  You should find after using the plugin that whenever you move the mouse over object pixels, the pixel value corresponds to the correct measurement in the table (unless I've made a mistake) - even if the pixel appears black.

To improve the appearance because the volumes are very different between objects you are likely to have to adjust the brightness/contrast settings quite a lot - specifically, keep the Minimum slider low and reduce the Maximum - otherwise small volumes will appear as black.  Also, it is probably worth running Image -> Lookup Tables -> Fire to get something other than shades of gray (or something else like Royal or 6 shades... the Image -> Color -> Display LUTs can help find a good choice).

You could also find a lookup table (LUT) without any white in it, e.g. Physics and then with Image -> Color -> Edit LUT... manually modify the first LUT to be entry (i.e. the colour used to show all pixels with zero or the lowest values) to be white; this will help even low volumes to stand out from the background.

The best choice will really depend upon what you want to show with the figure, and how big the variation in volumes really is.  With ImageJ LUTs you are limited to 256 different colours - if you need more, deciding the visualisation will be a bit harder.

Hi Peter,

thanks a lot for the helpfull response. You#re absolutely right, the values of each pixels are the same, it just looks different coused of the colors.

I thought that the colors depend on the measured volume of each object but I couldn't find further informations about that in the desciption of the "object counter".

Best

Lukas