[ome-devel] ets/vsi files with scifio

[Sebastien Besson (Staff)]

Hi Manuel,

Thanks for your questions.

First of all, when selecting either a .vsi or an .ets file, the Bio-Formats API will detect and group all files associated to both the macro image and the pyramidal images. There is no contract ensuring that the first image will correspond to the selected file as this mapping is practically complex to achieve across the set of supported formats - see this Github issue [1] for a related discussion.

The IFormatReader.setFlattenedResolutions API controls whether each pyramidal subimage will be detected as n separate series or as one series with n levels of resolutions. In the latter case, each sub-resolution of the subimage can be selected via the IFormatReader.setResolution API.

As far as we know, porting the resolution API was still on the roadmap of SCIFIO [2] which is why it might not exposed in the current interface. To get more detailed information, it might be worth enquiring directly using the ImageJ forum [3] which is the recommended way to get in touch with the SCIFIO developers.

Best,
Sebastien

[1] https://github.com/openmicroscopy/bioformats/issues/2309
[2] https://github.com/scifio/scifio/issues/43
[3] http://forum.imagej.net/

> On 25 Nov 2016, at 09:27, Manuel Stritt <manuel.stritt at actelion.com> wrote:
>
>
> Hello together,
>
> the VSI/ETS images might contain several nested images, e.g. one overview images and several high-res 'sub-images' (the ets files).
> If one opens an ETS file with scifio reader it opens not the selected ETS (sub-)image, bit instead it refers to the assigned VSI image which will open
> the first (or overview) sub-image - which might be different to the selected ETS image.
>
> Referring to
> http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-July/005506.html
>
> the solution is to set
> reader.setFlattenedResolutions('false');
>
> however, this only holds for a loci.formats.ImageReader, not for a io.scif.Reader.
>
> Is there a solution for scifio as well?
>
> Or - can I create a loci ImageReader and wrap it as a scifio reader (I read about a SCIFIOReader wrapper class, but can't find it anywhere).
>
> Thanks for your help!
>
> Regards,
> Manuel
>
>
>
>
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