Unable to open Nikon ND2 with Bio-Formats

Hi all,

I am using FIJI and trying to open .ND2 files with Bio-Formats. My stacks have 139 slices and no series, but when I open them with Bio-Formats it offers me 6 series, all of which open 92 slices when opened and all of these slices are black with no signal.

I have tried changing the settings in Bio-Formats to disable chunkmap and to use the Nikon library to open, same thing. I am able to open these images with the Nikon ND2 plugin for ImageJ, but I am then unable to do any processing on the images (max projections etc.) because ImageJ doesn’t work with that plugins image window. They also open fine in Nikon’s NIS viewer.

What else can I try to open these files in ImageJ/FIJI?

Thank you everyone!

I’m sure the Bio-Formats team would be happy to take a look if you could submit a problem image to http://qa.openmicroscopy.org.uk/qa/upload/ or otherwise make it available to OME. Ideal would be an image that can be made public but we can also keep it confidential if need be.

Which model of acquisition system acquired the images? Can you provide a screenshot from Nikon’s NIS viewer that shows what you’d hoped to see in FIJI?

Thank you, sorry for the late reply! It’s a bit difficult to submit an image as they’re 4.5 GB each, and I’m also getting “We’re sorry. SWFUpload could not load.” and can’t upload images on that site. I’m using Chrome so I believe Flash support should be inbuilt.

Anyway, I can open the images fine with the ND2 viewer plugin by Nikon, but this seems to have it’s own way of rendering the image (similar to a virtual stack? there’s a long delay when scrolling through z) and I can’t use any ImageJ functions on the image.

Seems to be the same as this issue:

Hi @GabrielH, do you know which version of NIS you sued to acquire the images?
If you send me a private message with an email address then I can arrange to send FTP details for submitting larger files.

Sorry again for the lack of replies - I have solved this issue by not using ImageJ. I am using a machine that has a registered copy of NIS elements instead.

If you would like to debug the issue though, as I imagine others will have the same experience, I can still send you an example file.

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Good to hear you have been able to find a work around. If your still able to send a sample file for testing though that would be great. If its greater than 2GB then send me a message with your email and I’ll arrange the ftp details for you.