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grishkam / QuickFigures

QuickFigures is a toolset for creating scientific figures see publication for details
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Question: Is it possible to add a custom lookup table for a channel? #16

Open boydcpeters opened 2 months ago

boydcpeters commented 2 months ago

First of all, thank you very much for developing this fantastic tool.

I have some single-channel images that would be better visualized with the help of another lookup table than currently available. I would like to pseudocolour them with the Fiji "Fire" lookup table or the "mpl-magma" lookup table. Is it possible in QuickFigures to add a custom lookup table and use this to colour a channel? If so, how would one do this? I couldn't find anything about it in the documentation, so I thought I would ask.

The file with the "mpl-magma" lookup table can be found at "Fiji. applutsmpl-magma.lut." I could not find the "Fire" lookup table, but they look very similar, so it would be great if I could use the "mpl-magma" lookup table.

grishkam commented 2 months ago

Thanks for the feedback. I will work on this. If you apply the lookup table to an ImageJ image before using QuickFigures to make a figure and save as tiff, the lookup table should still be there when figure is made. Let me know if this method does not work perfectly. Best, G

On Wed, Sep 4, 2024 at 3:50 AM boydcpeters @.***> wrote:

First of all, thank you very much for developing this fantastic tool.

I have some single-channel images that would be better visualized with the help of another lookup table than currently available. I would like to pseudocolour them with the Fiji "Fire" lookup table or the "mpl-magma" lookup table. Is it possible in QuickFigures to add a custom lookup table and use this to colour a channel? If so, how would one do this? I couldn't find anything about it in the documentation, so I thought I would ask.

The file with the "mpl-magma" lookup table can be found at "Fiji. applutsmpl-magma.lut." I could not find the "Fire" lookup table, but they look very similar, so it would be great if I could use the "mpl-magma" lookup table.

— Reply to this email directly, view it on GitHub https://github.com/grishkam/QuickFigures/issues/16, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEHSU4MOI3C63IEQCP5OKEDZU23TTAVCNFSM6AAAAABNTWS4G2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGUYDINJXGEZDEOI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

boydcpeters commented 2 months ago

Thanks for the quick reply!

I just tried out your suggestion. I saved my image with the "mpl-magma" LUT as a tiff file. Then I closed the image and opened it again with Fiji and it immediately showed the "mpl-magma" LUT.

However, when I start QuickFigures and create a new worksheet using `File>New>Empty Worksheet" and drag my saved tiff to the worksheet, it converts the LUT to the grey-scale LUT. See the attached screenshot:

screenshot_github

I have the following QuickFigures Messages:

QuickFigures toolbar opening
problem with lut arrays
 Was asked to change color for channel '0' but channel numbering starts from 1
Checking for size warning

There might be a problem with my channel naming. Any idea how to fix this?