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

[David Gault (Staff)]

Hi Kai,

Thank you for helping to investigate this further. When using the macro you attached I see the LUT being used correctly for both of the imports. For TIFF and OME-TIFF this works for me with the latest Bio-Formats so long as the color mode selected is ‘Default’ (which is correct with the macro). However the ICS and CH5 conversion I am seeing the grayscale upon import so there does appear to be an issue here that requires further investigating. I will update the Trello card and continue to debug the export process.

With Thanks,
David Gault

On 5 Nov 2018, at 16:48, Kai Schleicher <kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch>> wrote:

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.tif");
// does  not work with bio-formats importer
run("Bio-Formats Importer", "open=/home/kai/Desktop/m51_cool.tif autoscale color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
// but works with Imagej open
open("/home/kai/Desktop/m51_cool.tif");$


The University of Dundee is a registered Scottish Charity, No: SC015096
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20181107/5a1b6c87/attachment.html>