[ome-users] "stitch tiles" option not used for some tiled acquisitions from Zeiss LSM700

[David Gault (Staff)]

Hi Kai,

>From debugging the sample files it would appear that there are differences in the metadata between the two filesets.
Images acquired in multi-position mode have the positions of the acquisitions are stored as dimension P, and when images are acquired in tile-scan mode the positions of the tiles are stored as dimension M.

The first file which imported as a series of tiles was parsed to read a dimension P of 1 and dimension M of 20.
The second file which imported as you expected had a dimension P of 2 and dimension M of 1.

It would look as though there has been some minor difference in the acquisition which is resulting in different metadata fields being used.

With Thanks,
David Gault

On 27 Jul 2017, at 12:55, Kai Schleicher <kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch>> wrote:


Hi,

I was approached by one of our users who reported that recently some tile scans recorded at our Zeiss LSM700 inverted confocal do not import as "stitched" any more<https://demo.openmicroscopy.org/webclient/?show=image-1185>. Other images that where acquired with the exact same settings however imported fine<https://demo.openmicroscopy.org/webclient/?show=image-1231%7Cimage-1232>.

I think that the images are not actually stitched, as this option is not available in the version of acquisition software that was used.

Opening the files with FIJI/Bio-formats having the "stitch tiles" option checked works well.

When you compare the images, do you find a difference that maybe led OMERO to not use the "stitched tiles" option in some cases?

You can find all images on your demo server with Dataset ID 105<https://demo.openmicroscopy.org/webclient/?show=dataset-105>.

Thanks for your help and greetings from Basel,
Kai

--
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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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