ND2: Image stack lost for image with small dimensions

[dgault]

Issue was raised on forum thread https://forum.image.sc/t/can-not-read-nd2-image-stack-when-image-dimension-is-small/68155 but no sample file reproducing the issue is available as of yet.

The issue reports that when opening an image stack (in this case 5 planes) with a small image (50 x 50) then the image stack is lost and only a single plane is displayed. The same issue does not occur if the image is slightly larger (100 x 106). This was reported with Bio-Formats 6.10.0.

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/can-not-read-nd2-image-stack-when-image-dimension-is-small/68155/2

[denglabpku]

Hi Gault, Here is Zuhui. I uploaded the ND2 file for your testing. Please rename the PNG suffix to ND2 after you download it, because I found ND2 is not supported to upload.

[melissalinkert]

As noted in https://github.com/ome/bioformats/pull/3863, a temporary solution to this problem is to set the nativend2.chunkmap option to false as described here:

https://docs.openmicroscopy.org/bio-formats/6.9.1/formats/options.html#usage

[Borease]

As noted in #3863, a temporary solution to this problem is to set the nativend2.chunkmap option to false as described here:

https://docs.openmicroscopy.org/bio-formats/6.9.1/formats/options.html#usage

Hi melissalinkert

Thank you for your help. I can open the file correctly right now.