[ome-devel] Can I Add Thumbnails to BioFormats .ome.tiff File

[David Gault (Staff)]

Hi Michael,

Currently the OME Data Model does not specifically support the storing of thumbnails although this is something that we would like to look into specifying in the future.

Within the FormatTools utility class you can find the openThumbBytes method which provides a default implementation of generating a thumbnail from an existing image. The implementation can vary for different format readers but the default behaviour is to scale the image to a size of 128 x 128:
http://downloads.openmicroscopy.org/bio-formats/5.5.2/api/loci/formats/FormatTools.html#openThumbBytes-loci.formats.IFormatReader-int- <http://downloads.openmicroscopy.org/bio-formats/5.5.2/api/loci/formats/FormatTools.html#openThumbBytes-loci.formats.IFormatReader-int->

Additionally for TIFF format readers the default behaviour checks each TIFF IFD for the tag ‘IFD.NEW_SUBFILE_TYPE’. If the tag has a value of 1 then the IFD is added to a list of thumbnailIFDs rather than the standard IFD list. The 2 separate lists can then be read using ‘getIFDs’ and ‘getThumbnailIFDs’. If the thumbnailIFD list is present then it is used for openThumbBytes rather than the default FormatTools method above:
http://downloads.openmicroscopy.org/bio-formats/5.5.2/api/loci/formats/in/MinimalTiffReader.html#getThumbnailIFDs--
http://downloads.openmicroscopy.org/bio-formats/5.5.2/api/loci/formats/in/MinimalTiffReader.html#getIFDs--
http://downloads.openmicroscopy.org/bio-formats/5.5.2/api/loci/formats/in/MinimalTiffReader.html#openThumbBytes-int-

With Thanks,
David Gault

On 23 Jun 2017, at 12:38, Michael Ellis <michael.ellis at dsuk.biz<mailto:michael.ellis at dsuk.biz>> wrote:

I am exploring using BioFormat for our computer assisted microscope application.

I need to store XYCZT image files and need to store meta data such as pixel size, channel names, microscope and camera information along with the image. Images could be large and I also would like to implement a gallery view that can display visual view of a whole directory of images.

Is there a way to store a thumbnail images when saving an image file in .ome.tiff file that can be easily and quickly recovered from the image file for the purposes of displaying a gallery of images?

Even better, are there any operating system extensions that allow this thumbnail to be accessible such that the thumbnail is viewable in the operating systems default file finder/browser… thus obviating the need for me to implement a graphic gallery of images?

Michael Ellis (Managing Director)
Digital Scientific UK Ltd.
http://www.dsuk.biz

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