[ome-users] nd2 files from Nikon DS-Fi3 camera are not read correctly

[MEYENHOFER Felix]

Hey David

so here is the file that made me believe:
https://drive.switch.ch/index.php/s/zgxUk4c98loQTQJ

it turns out the file above is 3x8bit and the file I sent initially is 9x8bit. So a normal RGB works (BF swaps green and red though).
Bio-Formats does seem to have trouble when each channel is saved in RGB.

Given that both images come from the save instrument I jumped to the conclusion that the BF version of my colleague might have an impact, which was indeed different. I should have checked how the images are different given that one is 3 times lighter - dah - my bad, should have done that test before making claims, sorry.

Best

Felix



On 12 Oct 2018, at 14:48 , David Gault (Staff) <d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>> wrote:

Hi Felix,

Thank you for the update, we have made a number of updates to the nd2 reader in that time, especially in the 5.7 releases, so it may be possible that there is a regression.
I retested the original file that you had linked with 5.7.0 and a number of other releases but the issue still appears to be present in that particular file, would you be able to test if that file works as expected on your colleagues setup?

With Thanks,
David Gault

On 12 Oct 2018, at 08:55, MEYENHOFER Felix <felix.meyenhofer at unifr.ch<mailto:felix.meyenhofer at unifr.ch>> wrote:

Hi David

by chance I found on a colleagues computer with an old version of Fiji and Bio-Formats, that the reading of the nd2 files did not cause any problems.

working version (of my colleague)
ImageJ 1.51.n (Java 1.8.0_66)
Bio-Formats 5.7.0

the version I used submitting this report:
ImageJ 1.52g (Java 1.8.0_44)
Bio-Formats: 5.9.2

So there seems to be a regression from 5.7.0 to 5.9.2
However I did not investigate the versions in between…

Best regards,

Felix


On 27 Sep 2018, at 16:01 , David Gault (Staff) <d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>> wrote:

Hi Felix,

Thank you for reporting this problem and providing a sample file. I have been able to test and reproduce the issue as you described and it does indeed appear to be a bug.
I have opened a Trello card on the Bio-Formats board with the details and some of the initial investigation:
https://trello.com/c/EtOwZ7MH/283-nd2-incorrect-channels-and-pixel-data

With Thanks,
David Gault

On 26 Sep 2018, at 09:28, MEYENHOFER Felix <felix.meyenhofer at unifr.ch<mailto:felix.meyenhofer at unifr.ch>> wrote:

Dear OMERO Team

The following image causes problems when I try to open it using Fiji and Bio-Formats. Bellow is the image shown with the NIS Elements Viewer.

<Screen Shot 2018-09-26 at 10.14.16.png>


The window that is produced by Fiji shows only a part of the original image.
<Screen Shot 2018-09-26 at 10.17.13.png>


A closer look, shows that the C and X-Y dimensions seem to be messed up.
<Screen Shot 2018-09-26 at 10.17.34.png>

Finally the parsing of the metadata seems to have trouble too, given that the colors are not coherent with the image acquisition and given that the scale factor too seems to be missing in the displayed image in Fiji.
The original file can be found in the following link:
https://drive.switch.ch/index.php/s/QsroyTOOq6cDQXy

Is there a work-around, or could you confirm this being a bug?

Best regards,

Felix
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