Wrong image dimensions on FIJI when reading nd2 files



Good afternoon,

I acquired a batch of images with exactly the same settings using a Nikon C2 confocal system in the past month and a fixed pixel to micron ration for all of them – independently of channels. However, when I read my .nd2 files using Bio-Formats plugin, sometimes the Pixel width value doesn’t match the Pixel height.

Hence, it affects when using analysis tools such as “Analyze particles” and when saving the images from individual channels as tifs, jpegs, etc.

Interestingly, for some of the images the values that appear are the correct ones, for others it varies from 2.618 to 2.625, even though all the acquisitions were performed with the same settings. It is important to note that Nikon elements shows the same values for for pixel height and width, regardless of what is read on Fiji.

I know from my acquisition parameters that the Pixel height value is the correct one, and it is possible to fix the problem by inputting the appropriate value in the image properties. Nevertheless, I was wondering if you have any idea about why this is happening and if there is a package out there that can automatically fix it.

Thanks for the help,




The mismatch of Pixel height and width values is not something we were aware of so thank for bringing it to our attention. Can you confirm which version of Bio-Formats you are using? (Can be found using Help -> About Plugins -> Bio-Formats Plugins)

Also if you had a sample file which displays this issue would you be able to upload it to the below link for testing?


David Gault


Hi, David,

Thanks for the response. I have seen this using Bio-Formats releases 5.1.8 and 5.1.10 on Windows and 5.1.3 on Mac.

I uploaded two sets of images that present the error. Each set presents a value for pixel width, even though the acquisition parameters were exactly the same for both of them and the pixel height value is the same (and the correct one).

Thanks for the help,




Thank you for submitting your files to our QA server.
We were able to reproduce the issue in the latest version of Bio-Formats(5.4.0) on Fiji.

We have created a card on this front,

and the issue is currently under investigation.