[ome-users] Import plate data from the FEI MORE as screen in OMERO

[Munro, Ian]

Dear Kai


Some time ago I wrote some example code to write plate data (from  arrays in memory ) into an ome-tiff
<https://g>

Maybe you could adapt that either by reading your individual tiffs into memory or possibly by using it to write an accompanying xml file to go with your tiffs.


https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/utils/FileWriteSPW.java

[https://avatars0.githubusercontent.com/u/975861?s=400&v=4]<https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/utils/FileWriteSPW.java>

openmicroscopy/bioformats<https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/utils/FileWriteSPW.java>
github.com
bioformats - Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the ...




I'm not sure the second option is viable - hopefully somebody has a better idea.


I hope that's of some help.


Best Wishes


Ian



________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of Kai Schleicher <kai.schleicher at unibas.ch>
Sent: 25 July 2018 16:22:31
To: ome-users at lists.openmicroscopy.org.uk
Subject: [ome-users] Import plate data from the FEI MORE as screen in OMERO


Dear OME team,

I acquired a few images in a 96 plate<https://filesender.switch.ch/filesender/?vid=7ada3ba0-e2e2-9629-ca18-00001996de3c> (2 Wells, 4 images/well, 3 channels/ image) on an automated Widefield system (FEI MORE, using the Live Acquisition (LA) software v 2.6).

The data is saved as single tiffs with metadata. Additionally it saves one xml file per well that contains information about the sites imaged.

I would like to import this data in OMERO in the screen/plate format.

Both the image metadata and the xml file is supposedly compatible with the ome data model, but I did not yet find a configuration in which these images can be imported into OMERO as a plate/screen.

My question is hence if you could have a look and see if I am somewhat close to achieve my goal :)

Since its probably not so easy, could you let me know what else would be needed for OMERO to import these images as a screen?

Thanks and cheers,
Kai

--
>>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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