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Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
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ND2: Inverted LUT for RGB images #3761

Open dgault opened 2 years ago

dgault commented 2 years ago

Issue was raised on forum thread https://forum.image.sc/t/nd2-rgb-import-issue/60901 and a sample file reproducing the issue is available on Zenodo - https://zenodo.org/record/5772393#.YbNTrPnP1Zc

When the ND2 file is opened using Bio-Formats 6.8.0 and Composite mode via the FIJI plugin the resulting image does not match the colour seen when importing into NIS Elements Viewer

imagesc-bot commented 2 years ago

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

https://forum.image.sc/t/nd2-rgb-import-issue/60901/7

imagesc-bot commented 9 months ago

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

https://forum.image.sc/t/nd2-file-opening-up-as-greyscale-instead-of-correct-colors-in-fiji/88960/5

dgault commented 9 months ago

An additional report of this issue has been received on forum thread https://forum.image.sc/t/nd2-file-opening-up-as-greyscale-instead-of-correct-colors-in-fiji/88960/5

A sample file reproducing the issue is available at https://zenodo.org/records/10277961?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6Ijg4YTBkZmZmLTA4ZDctNDFlZi04Mzk5LWQ0YTMwOGE3MzE4ZCIsImRhdGEiOnt9LCJyYW5kb20iOiIzZTA4ZjI2ZDc3N2U5YzBkNzQ3NjhiNDVhNzEzMzBjOSJ9.Vw5Cqek98Sacs87fKlJKujS0o4qP1wt8g7vV4FercXLOa1NoDb8ASdnwFJucMn2B9SH0ywBrs-QKnkOALJKqOA

I was able to reproduce the same issue reported by the user using Bio-Formats 7.0.1 with the image colors showing incorrectly

imagesc-bot commented 9 months ago

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

https://forum.image.sc/t/nd2-file-opening-up-as-greyscale-instead-of-correct-colors-in-fiji/88960/7

dgault commented 1 month ago

An additional report of this issue has been received on forum thread https://forum.image.sc/t/nd2-rgb-import-issue/60901/7

A sample file and comparison tiff are available at https://zenodo.org/records/12734440

I was able to reproduce the same issue reported by the user using Bio-Formats 7.3.1 with the the red and blue channel appearing to be swapped when opening in composite mode with the Bio-Formats plugin in FIJI

imagesc-bot commented 1 month ago

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

https://forum.image.sc/t/nd2-rgb-import-issue/60901/12