Voxel counter: strange numbers output

Hi all,

I have a thresholded stack, with calibration for pixel size. An example slice is attached. Also attached is the output by the plugin Voxel Counter. Some observations:

The column headed ‘Area’ has a value for each slice that gives the thresholded (red) area for that slice, in µm^2. This seems correct.

The figure for ‘Thresholded voxels’ at the bottom of the columns is way too low. I have calculated the thresholded pixels from the area in each slice x the voxel height / voxel volume. The correct figure is around 16000. The 250 figureappears to be the sum of the areas in each slice.

The figure for ‘Average voxels per slice’ is actually average area per slice.

‘Total ROI Voxels’ and ‘Voxels in stack’ is correct, as is ‘Voxel size’.

‘Thresholded volume’ reads 1.33 µm^3 - I have calculated that this should be 84.9 µm^3. I haven’t worked out where 1.33 comes from yet {Edit: I guess this is 250 x voxel volume}. ‘Average volume per slice’ is similarly wrong, but the last two entries (Volume of stack’ etc. are correct.

Very frustrating and time consuming! Any ideas what I or Voxel Counter needs to do differently?




How very queer. After a night’s sleep the output from the same plugin on the same file is very different, and I think as it should be (see attached). I’d still be interested in knowing what happened.

This erratic behaviour might be something to do with whether the image has its own pixel size values, or if it is borrowing them by having the ‘global’ option ticked on another image.


perhaps it’s time to consult the User-Guide:

"XXIII Global Calibrations
Calibration settings related to spatial (pixel width, height and voxel
depth), temporal (frame interval) and luminance (brightness) information
can be set globally, i.e., can be applied to all images opened during
the current session instead of just the active image. The Global flag
can be set in three dialog prompts:

  1. Image . Properties. . . [P] (pixel width, height, voxel depth, frame
  2. Analyze . Set Scale. . . (pixel width and height)
  3. Analyze . Calibrate. . . (pixel intensity)
    Once Global calibration is set, a ‘(G)’ is displayed in all image titles
    until ImageJ is closed. A warning message is displayed when a calibrated
    image with conflicting calibration is opened and the Global option is
    Choose Disable Global Calibration to stop using global settings or
    Disable these Messages to keep respecting global settings, ignoring the
    calibration of the newly open image."



Hi Herbie,

Thanks for taking the time.

Firstly, I have little doubt that the User Guide contains the answer to many problems that are raised on this forum, possibly including this one. However, if we all agree that it is not feasible to read the guide from start to end each time we have a problem, then we need some inkling on which section to read. It is only in the past hour that I have identified Global calibration as a potential area of interest, so perhaps you are right, now might be a good time to consult the user guide.

Secondly, having looked at that section of the User Guide there is nothing there that indicates Global calibration would cause Voxel Counter to behave inconsistently, so this would have been zero help in understanding my issue.

I realise it’s easy sometimes to wrongly read the tone of an online post, and maybe you weren’t being condescending, but I feel that I have been ‘told off’ here (I have noticed your weariness with people not reading the documentation on other posts). To me, a forum like this is a meeting place for people who want to learn something, and people who like helping other people to learn. If I’m just going to be made to feel that I’m wasting your time by posting then what is the point of a forum?

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You are welcome!

I thought the details of the guide-excerpt could have helped explaining the “erratic behaviour”, as you called it. Maybe I was wrong.

Anyway, interesting statements about helping yourself and helping others.