[ome-users] Bio-formats exporter does not store custom LUT applied in ImageJ

[David Gault (Staff)]

Hi Kai,

Thank you for raising this issue, using the process you followed should be expected to work and does appear to be fine when exporting to other formats such as TIFF.
Unfortunately it looks like this is a bug in the ICSWriter which is not saving the custom LUT values during the export. I have opened a Bio-Formats Trello card for this bug at https://trello.com/c/LzWW3y7F/291-icswriter-not-preserving-luts

With Thanks,
David Gault

On 2 Nov 2018, at 17:47, Kai Schleicher <kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch>> wrote:

Dear OME team,

I wish to apply a custom LUT in ImageJ and then save the image as ICS-1 using Bio-formats.

When I import the image again with Bio-formats, it does not show the LUT (see imageJ macro in below quote to reproduce the steps).

Did I miss an option during import, or is there maybe a different way the LUT should be applied to the image for the exporter to save it?

Thanks and cheers from Basel,
Kai

run("M51 Galaxy (177K, 16-bits)");
run("cool", "display=m51.tif view=net.imagej.display.DefaultDatasetView at 7a6b36cd");
run("Bio-Formats Exporter", "save=/home/kai/Desktop/m51_cool.ids");
run("Bio-Formats Importer", "open=/home/kai/Desktop/m51_cool.ids autoscale color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");

--
Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22 50 (central)<<
Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) | kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch> | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch>

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