ND2 to TIFF with correct voxel depth


I am trying to convert a ND2 file of a colored neuron to TIFF or v3draw with Bio-formats in imageJ. The issue I am having is when I convert it the voxel depth becomes 1, but I need it to keep the original depth, so I can use the image to reconstruct and analyse the neuron in Vaa3D. Depth is a important factor to calculate all the characteristics. Can somebody help me? I am a noob using these programs, so no explanation is too long. Thanks in advance!

Hi @Jim_Hagemann, are the correct values listed anywhere in the metadata when you open the Show Info window in ImageJ? If possible it would be great if you could upload a sample file showing the issue to https://www.openmicroscopy.org/qa2/qa/upload/

Hi @dgault, thank you for the response. Sadly I can not upload the files, because both the TIFF and ND2 are around 5 GB. I have uploaded the images below with the metadata and the opened file. The green image is the ND2 file and the other is that file converted into TIFF. As you can see the voxel depth has become 1 after converting with Bio-formats exporter. I hope this helps to visualize the problem.

Thanks Jim, that does help, this is actually due to the fact that the standard TIFF tags only provide support for physical size/resolution in X and Y but there is no relevant tag for Z which causes that piece of metadata to be lost in conversion. If you export to .ome.tiff instead then this extra metadata will be retained in the OME-XML metadata and the voxel size will be correct when reimporting.

Thanks for your help!