Open Microscopy Environment

Hello,

I'm a new user of ImageJ, and I would like to open ND2 (nikon elements) files with bioformats. My images have 11 z stacks, and three color channels at each stack. Whenever I try to open one with the Bio-Formats importer, it breaks the nd2 file into 11 series each containing 3 planes. This results in opening 11 separate windows for each z plane. In each window, I can scroll through the 3 color channels. I'd much rather have 3 windows open (one for each channel) and have the ability to scroll through the z planes, but I have not figured out a way to do so.

Additionally, I would eventually like to batch convert all of my nd2 files into tiffs. Ideally, I'd like 33 tiffs from each nd2 file (each z plane in all 3 colors). However, when I use ImageJ's built in batch converter with bioformats, I get a single tiff for each nd2 file. These tiff contain only the first z plane of each of the 3 color channels.

Is there a way to get around any of these issues? Any help would be greatly appreciated.

Thanks!

Which version of bioformats are you using with ImageJ? The last updates which probably affect you were made for version 4.4.7, so if you're using an earlier version it's definitely worth updating and retesting to see if this fixes things. If you're already using the latest version (4.4.8), then disregard this.

If you would like to upload an example image demonstrating the problem to our QA system
(https://www.openmicroscopy.org/qa2/qa/upload/) then we can take a close look at it and see what's going wrong. If you're using a new version of Nikon Elements, it's possible that there is a variant of the file format we don't yet properly handle, and with an example image we can add support for it.

Regards,
Roger Leigh

Hello Roger,

I ensured that I had the latest version of bioformats and tried again without luck. I've uploaded a file (SampleND2-ChrisL.nd2) at the link you provided. Let me know if you got it. I'm happy to provide more if you'd like.

Thank you!

Thanks Chris,

I've taken a look at the file, and like yourself I also see 11 separate images. Each of these images has dimensions of 1392x1040x1x1x3 (x/y/z/t/c).

Could you confirm for me exactly what the expected dimensions of the image are? 1392x1040x11x1x3? Or are we computing any other dimensions incorrectly?

Regards,
Roger Leigh

We have a ticket tracking this issue (#11305, Bug: NativeND2Reader computing image dimensions incorrectly https://trac.openmicroscopy.org.uk/ome/ticket/11305). I added you so that you'll be notified when this is fixed; I can remove you on the CC if you'd rather not be.

Regards,
Roger

Hi Roger,

Yes, those are the correct dimensions. Thanks for opening the ticket adding me on the CC. Let me know if I can provide any further information.

Best,
Chris