Open Microscopy Environment

Hi,

After updating Fiji or ImageJ, wrong LUTs will be shown when opening .lif images with BioFormats.

All channels show the same color as that from the first channel if more than one channel are in one image.

https://imgur.com/a/lGQpY

I have no idea whether it is caused by updating the imageJ or by Bio-Formats. I tried to find an answer within
ImageJ forum but got no response. Hopefully, your team could give us some assistance. Thanks!

ching

Hi Ching,

We haven't made any recent updates to that particular format so it may be due to the options used in the importer. In the Bio-Formats Importer window what option is selected for Colour Mode?

Also if you have a sample file showing this problem you can upload it to https://www.openmicroscopy.org/qa2/qa/upload/ and I can further test the issue.

David Gault

Thanks for the reply David,
I have uploaded a test.lif to the place you mentioned. Please have a look at it.

We have used the "Default" color mode In the Bio-Formats Importer window no matter which version of ImageJ
or Bio-Formats package was used. We currently need to set the color mode as "Colorized" in order to get the
correct channel LUTs after updating the Fiji or ImageJ.

Best,
ching

Thank you Ching, we successfully received the file you uploaded. I shall test it to see what has changed between the Default and Colorised modes.

David Gault

As a follow up to this investigation. I have been able to reproduce the issue using the sample file provided.

With an older ImageJ version the file opens by default with each channel displaying a separate colour. Replacing the Bio-Formats jars with more recent releases produces the same behaviour (version used was 1.51h from 30 May 2017 FIJI, final Java 6 version)

With a later ImageJ version (1.51n) the QA file opens with the same colour in each channel. Replacing the Bio-Formats version with previous versions does not affect the behaviour. Changing the colour mode in the Bio-Formats importer to Colourised does however display the correct colours for each channel.

This issue appears to be a change in how the default colour mode is handled between the Java6 FIJI and Java8 FIJI. I have opened a Trello card to further investigate if any changes are required in the Bio-Formats plugin to the default behaviour. https://trello.com/c/8BQ2ViRo/212-fiji- ... olour-mode

Hi David,

Is the new version of bio-formats-5-8-0 still not able to show the correct LUTs when opening the .lif images?

Best,
ching

Hi Ching,

Im afraid we did not have a fix for this particular issue in the latest 5.8.0 release. This week we will be evaluating and prioritizing cards on the Trello board including https://trello.com/c/8BQ2ViRo/212-lif-c ... g-metadata for upcoming releases.