Open Microscopy Environment

Hi team,

I chanced upon (maybe add a mention of it in the docs?) the omero export capability in the cli which is extremely useful for a number of folks in my group. I have a few questions related to it:

1) when I export an image with rich OME-XML metadata, only a small amount of that appears to make it into the generated ome.tif file. At least when looking at that with showinf or when loading into imagej/fiji, very little shows up.

2) the --iterate is great for Dataset. Any plans of adding the capability to use that for Plate and/or Screen?

3) this question is a bit out there: any thought to make it do some kind of ROI handling e.g. if the image has ROIs, then have the option to only export the ROIs as individual ome.tif's?

4) finally, I noticed that this cli export as OME-TIFF works fine even when in the webclient, I only have the options to export as tiff, png, or jpg. This happens e.g. for images in SPW. Since the capability to export as ome.tiff clearly exists, any thought of enabling that capability in the webclient/insight client as well?

Always great to find another useful nugget in OMERO and sorry that I always want more .....
Cheers,
- Damir

dsudar wrote:Hi team,

Hi Damir,

I chanced upon (maybe add a mention of it in the docs?) the omero export capability in the cli which is extremely useful for a number of folks in my group.

The new webpage has: https://www.openmicroscopy.org/omero/export/ but https://docs.openmicroscopy.org/omero/5.3.3/users/cli/index.html?highlight=command%20line%20interface (minimally) should add a mention.

I have a few questions related to it:

1) when I export an image with rich OME-XML metadata, only a small amount of that appears to make it into the generated ome.tif file. At least when looking at that with showinf or when loading into imagej/fiji, very little shows up.

Yes. At the moment, the use is intended mostly for getting the binary data out of OMERO not for all the related metadata, though that's something we're interested in adding.

2) the --iterate is great for Dataset. Any plans of adding the capability to use that for Plate and/or Screen?

Added to https://trello.com/c/22XfjucX/7-export-re-import.

3) this question is a bit out there: any thought to make it do some kind of ROI handling e.g. if the image has ROIs, then have the option to only export the ROIs as individual ome.tif's?

Ditto.

4) finally, I noticed that this cli export as OME-TIFF works fine even when in the webclient, I only have the options to export as tiff, png, or jpg. This happens e.g. for images in SPW. Since the capability to export as ome.tiff clearly exists, any thought of enabling that capability in the webclient/insight client as well?

I'm not sure what's happening there, and filed https://trello.com/c/bxkT6Jla/107-export-ome-tiff-export-disabled-in-web-when-available-from-cli for someone to take a look.

All the best.
~Josh.

Hi Damir,

To enable export of SPW images in webclient/Insight, you need to configure
https://docs.openmicroscopy.org/omero/5 ... ary-access.

Code: Select all

$ bin/omero config set omero.policy.binary_access '+read,+write,+image,+plate'


This will also enable the download of Original Image files.

In general, downloading of SPW original data is disabled because even a single image comes from the whole 'fileset' of SPW data (whole screen) so is likely quite large.

Even without configuring the omero.policy.binary_access, you can export SPW images as OME-TIFF by selecting the image(s) and running the Batch_Image_Export script, choosing Format: OME-TIFF.

Regards,

Will.

Hi Will,

Thanks for pointing me at that config setting (and the reminder about the batch export script). I had seen it long time ago but completely forgot about the existence. That works. I agree that in general one would not want to enable this since it enables downloading of entire plates/screens. Maybe another "permission level" could be considered for a future version which allows exports of OME-TIFs but does not allow downloading of the original data for entire plates/screens?

Cheers,
- Damir

Dear Damir,

Even without adjusting the server's access policy we should enable the export of individual fields as OME-TIFF from OMERO.web, we'll look into that, thank you.

It's worth mentioning that larger-scale remote data access is at least very much on our radar. For example, https://github.com/mtbc/omero-downloader is a proof-of-concept for resumable download/export of large screens. In export, that tool does the construction of the OME-TIFFs client-side to avoid burdening the server with everybody's enormous exports.

Cheers,
Mark

Hi Mark,

Great that you'll consider individual image/field OME-TIFF exports as part of the "default" policy of: '+read,+write,+image'. That makes perfect sense.

I'll have a look at omero-downloader. Thanks for directing me to it.

Cheers,
- Damir

Dear Damir,

Also note that Will has now opened https://github.com/openmicroscopy/openm ... /pull/5472 which should indeed allow OME-TIFF export of individual wells in OMERO.web for 5.4.0.

Cheers,
Mark