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ND2: Skewed image display #3661
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This issue has been mentioned on Image.sc Forum. There might be relevant details there: https://forum.image.sc/t/bfconvert-nd2-rgb-to-stack-of-tiff-grays-channels/48360/9 |
Hi @dgault I wanted to mention that I have observed the same issue. FYI:
Could you find already a solution? I have more example nd2 files if needed and can provide you a download link. Thanks and bests. |
Hi @loicsauteur, thank you for the additional details, unfortunately we do not yet have a solution for this particular bug. If you have any sample files showing the issue it would always be helpful. |
Please find 9 nd2 files with following link (will expire): |
Thanks @loicsauteur for the sample images, they are a great help. With the latest Bio-Formats (6.6.1) I am seeing the skewing issue pretty clearly in 6 of them, however |
Yes, 6 of them have the described skewing error.
(Edit) |
An additional report of this issue has been received on forum thread: https://forum.image.sc/t/problem-with-nd2-large-image-stitch-opening-strange-with-bioformats-on-fiji/67319/5 A sample image showing the skewed image was provided and the error could be reproduced using Bio-Formats 6.9.1. |
This issue has been mentioned on Image.sc Forum. There might be relevant details there: |
This issue has been mentioned on Image.sc Forum. There might be relevant details there: |
An additional report of this issue with 5 sample files showing the same skewed displayed can be found at 4 of the files show the same issue and can be reproduced with Bio-Formats 7.3.1. The last file ending |
Image was raised on imagesc thread https://forum.image.sc/t/bfconvert-nd2-rgb-to-stack-of-tiff-grays-channels/48360/7
A sample file reproducing the issue with Bio-Formats 6.6.0 can be found at https://github.com/bioimage-analysis/Files/blob/bd6977bbfb5081ba74d6202b3faf5b92ae1529f2/error.nd2
Opening the file with Elements Viewer suggests that the basic metadata (dimensions, pixel type etc) are correct.
In Elements Viewer the image displays as:
With Bio-Formats the image is displaying as:
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