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General user discussion about using the OMERO platform to its fullest. Please ask new questions at https://forum.image.sc/tags/omero
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Historical discussions about OMERO. Please look for and ask new questions at https://forum.image.sc/tags/omero

There are workflow guides for various OMERO functions on our help site - http://help.openmicroscopy.org

You should find answers to any basic questions about using the clients there.


Postby sameh » Thu May 16, 2019 10:39 pm

Hello All Omero team,

I would like to understand how Omero converts pixel data into an ome-tiff format.

We have an image analysis workflow that uses the vtk format. We want to save the output images in ome.tiff.

We have the pixel data and image metadata from the vtks and we want to write that into an ometiff using the ometiffwriter class.

Do you have any documentation to guide us in our project?

thank you so much

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Re: ometiffwriter

Postby dgault » Fri May 17, 2019 9:54 am

Hi Sameh,

You can see the developer documentation here: https://docs.openmicroscopy.org/bio-for ... index.html. The examples it uses (https://docs.openmicroscopy.org/bio-for ... xport.html and https://docs.openmicroscopy.org/bio-for ... port2.html) are often converting from a format which is already able to be red by Bio-Formats so for a new format it will be slightly different.

One other option would be to create a Bio-Formats reader for the format, as you seem to be able to extract the pixel and metadata from the format already we would be happy to help you structure it into a new VTKReader for Bio-Formats. You can see some documentation on creating a new reader at https://docs.openmicroscopy.org/bio-for ... guide.html and the code for some of our existing readers is at https://github.com/openmicroscopy/biofo ... formats/in. If you have a specification or some sample code you can share we can offer some further guidance.

David Gault
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