Image type question using MorphoLIbJ

HI guys,

I have an 8-bit image with only 0 or 255 as a pixel value and want to run the following:

run("Distance Transform Watershed 3D", "distances=[Borgefors (3,4,5)] output=[16 bits] normalize dynamic=2 connectivity=6");

But I always get


which makes no sense to me. I honestly checked the image stats and it shows only 0 and 255 as pixel value and the image is an 8-bit.


So what do I miss here?

Image cab be found here:



When I open your .ome.tiff file, plot the histogram of the entire stack, and press the List button, I see that there’s one pixel with intensity 2 in your stack:


I don’t know where this value is coming from, but simply running a threshold again might solve your issue.


Hmmmm … And inside ZEN the CZI-File has only 0 and 255 as pixel values. But when I open it in Fiji there suddenly is one pixel with the value 2.

:astonished: that sounds to me like a #bio-formats issue then…

EDIT: for the record, the “wrong” pixel value of 2 is at position [193, 71, 112].

Hi Jan,

thanks, I found it in ZEN now as well … - therefore everything is fine with BioFormats.

I still have no clue where this comes from, since the segmentation function producing it only gives either 0 or 255 as return values by definition. And I cannot reproduce it anymore …

So I consider this question answered.

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