[ome-devel] Trello Bio-Formats 5.6.0 board closed / ImageJ BioFormats Image Importer Plugin

[David Gault (Staff)]

Hi Michael,

The rendering settings within OMERO are not saved onto the OME-TIFF itself. Within Bio-Formats the TIFF readers will read the image LUT from the TIFF IFD tag 320 ColorMap<https://www.awaresystems.be/imaging/tiff/tifftags/colormap.html>.
If you are writing the images using the TiffWriter in Bio-Formats then you can set this using the method setColorModel on TiffWriter.
Alternatively if you are using ImageJ with the Bio-Formats plugin then you can also save the LUT values applied in ImageJ using the Bio-Formats exporter.

With Thanks,
David Gault

On 23 Feb 2018, at 17:43, Michael Ellis <michael.ellis at dsuk.biz<mailto:michael.ellis at dsuk.biz>> wrote:

Dear all, I am using  BioFormats.jar package to save and restore images in .OME.TIF format.

Sometimes my image channels comprise pixels of unsigned short pixel format. I would like to be able to store within the image the values used for normalising the data for display purposes. Is there a standard way of storing this normalisation data (and or LUT data) in a .OME.TIF file?

I note that if I use the OMERO.insight program to save and restore 16 bit images saved in .OME.TIFF it appears to save normalisation levels, since the OMERO.insight has the option to save the colour palette adjustment settings. However if I download the ,OME.TIF file back to my desktop and open it with the ImageJ BioFormats importer, normalisation levels are lost, and when displaying the BioFormats OME metadata, there is nothing to indicate that any normalisation levels are being saved. It is as if the OMERO platform is saving those normalisation viewing parameter separately from the OME.TIF file

Any help gratefully appreciated!

Michael Ellis
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