Open Microscopy Environment

Hi

As a way of keeping meta data with our images and for archiving purposes we are considering using OME Tiff format.

Can I upload images using the python api and get them to be created as OME tiff programmatically? or do I have to upload - create a OME tiff then delete the original image? I'm assuming I would also have to upload first and then add meta data later? Or would the preferred way to be to create the OME Tiff using bioformats, add the meta data and then upload to OMERO?

Are there performance disadvantages to working with images in OMERO in OMERO tiff format?

I also see from the docs that we can only work with OME Tiffs using java and not the python API?

Sorry for the many questions.

Jonathan.

Hi Jonathan,

jwarren wrote:As a way of keeping meta data with our images and for archiving purposes we are considering using OME Tiff format.

Making sure I understand, you have images (previous JPEG, right) which you would like to have stored long-term in OME-TIFF, correct?

Can I upload images using the python api and get them to be created as OME tiff programmatically?

You can upload files from Python using the import API and then use the export API to retrieve OME-TIFF on the fly.

or do I have to upload - create a OME tiff then delete the original image?

I don't follow.

I'm assuming I would also have to upload first and then add meta data later?

You're talking about creating an OME-TIFF before hand and then importing that? It depends on your metadata. It's possible to put the metadata into the OME-XML in the OME-TIFF. However, you could of course add it via the API later as well.

Or would the preferred way to be to create the OME Tiff using bioformats, add the meta data and then upload to OMERO?

Hard to say. Do you have an indicative example you could give us? Is there a lot of variability?

Are there performance disadvantages to working with images in OMERO in OMERO tiff format?

Depends on what you are comparing to, i.e. what the concrete example is. I don't foresee a particular bottleneck in importing OME-TIFF to OMERO. Exporting (especially frequently) to OME-TIFF might be more of an issue, but again it depends.

I also see from the docs that we can only work with OME Tiffs using java and not the python API?

Which docs are you looking at? And to achieve what?

Sorry for the many questions.

No worries.

Jonathan.

~Josh