Nikon ND2 File Not Opening Correctly

[Cammyron]

Hi All,

I have an ND2 file that contains 3 tipe points, 2 stage positions, 2 channels and 34 z slices. It opens fine in the NIS viewer but when i open it with the latest version of the LOCI tools it shows me 3 series to pick from, all of which do not corespond to the data structure (not enough Z and no position information). If i open them as raw imagej stacks they contain bits of each of the stage positions.

happy to upload an example file if that helps out.

Cheers

Cameron Nowell

[rleigh]

Hi,

An example file would certainly help us to investigate the issue, thanks. We did get an ND2 file uploaded, but without any identifying name (QA #7899); is this your image? If it wasn't, you can upload a file here: https://www.openmicroscopy.org/qa2/qa/upload/ Assuming it was, I'd just like to confirm that it has the 3 time points, 2 positions, 2 channels and 34z that you mentioned, or if it differs.

With both 4.4.10 and 5.0.0-rc2, this shows as having:

Code: Select all

        Image count = 3
        RGB = false (1)
        Width = 1392
        Height = 1040
        SizeZ = 1
        SizeT = 1
        SizeC = 3
        Dimension order = XYCZT (certain)
        Pixel type = uint16

This doesn't look like what you're describing though since there's only one series, so maybe not your image?

Thanks,
Roger

[Cammyron]

Hi Roger,

That file isn't mine, i am uploading mine now. Its 500mb so might take a while

Cheers

Cam

[Cammyron]

Hi Roger,

Upload done (QA# 7908)

Cheers

cam

[rleigh]

Thanks for uploading the image. I've taken a look, and I can definitely see the problem you described. I have opened a ticket for this: https://trac.openmicroscopy.org.uk/ome/ticket/11997 . You should be copied on any changes to the ticket.


Thanks again,
Roger Leigh

[Cammyron]

Hi Guys,

has there been any progress on this big at all?

Cheers

Cam

[rleigh]

Dear Cam,

I'm afraid this bug is still present (tested with today's 5.0 and 5.1 builds). Since you reported the bug, an issue with ND2 field ordering has been fixed, but this unfortunately didn't affect the issue with the dimension sizes you were experiencing.


Regards,
Roger Leigh