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

[Kai Schleicher]

Hi David,

thank you for reproducing the problem.

I have tested the issue a bit further and found that the bio-formats 
exporter does actually save the LUT in some way.

It seems to rather be the importer that does not import it afterwards. 
Opening the image with ImageJ open instead works, see below macro code.

> 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");$

I have also tested several different formats of the Bio-formats exporter 
(ICS-1, ome.tif, tif, ch5), but importing an image with custom LUT also 
shows as grayscale.

Thanks for investigating and cheers,
Kai


On 11/5/18 5:01 PM, David Gault (Staff) wrote:
> 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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