Open Microscopy Environment

Hi,

We are developing tools for automated analysis with OMERO, the only interactive missing features missing from Omero are the possibility to see pixel values within the the image and the possibility to adjust a threshold (not performing it). Any idea if this can be done already or if these features are planned ?

Thanks

Thomas

Hi,

I'm afraid I don't quite understand your workflow or what tools you're using.

How are you running automated analysis with OMERO? Python scripts? Java client? Matlab?
When you say "interactive" do you mean a manual UI? E.g. iviewer? https://www.openmicroscopy.org/omero/iviewer/
You can enable reporting of pixel intensities that you mouse-over in iviewer using the cross-hairs + button.
You can also adjust rendering settings with or without saving them. Is that what you mean by "adjust a threshold (not performing it)"?

Regards,

Will.

Hi Will,

Thanks for your reply. We are currently developing tools to automate analysis of images stored in Omero, basically it is kinda batch ImageJ processing but using Omero instead of folders/files. As for interactive yes I mean manual, like ideally users find threshold within omero using any viewer/tool , put the value as key-value and we use this value to threshold the image and perform the analysis. It will be then easier to select the threshold within Omero than downloading the file into ImageJ and then find the threshold. We will give iviewer a try since it is quite close to what we want.

Best

Thomas

Hi Thomas,

You can Save the desired rendering settings in iviewer (or in the regular webclient viewer) and use that setting in your analysis, without necessarily needing to save it as a Map annotation.
Let us know if you need any help anyway.

Will