Open Microscopy Environment

Hi all,

I have been importing Olympus ScanR experiments into my Omero 4.4.9 installation. This works fine and they automatically show up as Screens in Insight. However, I can neither download the original files (even though I had chosen "Archive" upon importing), not can I Export as OME-TIFF... the individual images. Both options are greyed out. Even Save As ... (JPEG/PNG/TIFF) does not do anything but silently fails. All of the above works fine for images in "Projects" as opposed to images in "Screens". Any ideas?

And related but different: the Batch_Image_Export.py script does work kinda okay to export the image data from these HCS screens but there is no easy way to populate the list of image IDs in the script UI except by typing in the whole list. Pre-selecting a bunch of images does not get transferred into that dialog box the same way how it works for images in the Projects. And batch exporting a whole "dataset" is not possible since there is no "dataset ID" associated with a Plate Run, Plate, or Screen.

Thanks for any pointers,
- Damir

Hello Damir,

Unfortunately, 4.4.9 does not have the ability to archive plates on import and we’ve failed to make this clear in the UI. Apologies if this has led to any data loss. Ticket created: see http://trac.openmicroscopy.org.uk/ome/ticket/11837

This workflow is improved in OMERO-5 version of our software - in OMERO-5 we upload all original data to the server on import. We will be exposing the download of this original file from clients in OMERO-5 (currently work in progress).

We have previously disabled the OME-TIFF export for HCS data because a “valid” OME-TIFF image would include the whole plate. However, it seems that it’s now possible to export HCS images in OME-TIFF format using the Batch_Image_Export script, so we’ll look into enabling this in Insight too. Ticket created: http://trac.openmicroscopy.org.uk/ome/ticket/11836

The silent failure of the jpeg, png and tiff download is a bug in Insight - we have created a ticket to fix this - see http://trac.openmicroscopy.org.uk/ome/ticket/11834.
We can also address the passing of Image IDs from selected HCS wells to Scripts. http://trac.openmicroscopy.org.uk/ome/ticket/11835

A quicker fix for the Batch Image Export script would be to add “Plate” as a supported Data Type, allowing you to enter a single Plate ID to export all the images in a Plate. We have avoided this before because it has the potential to try and export a very large amount of data (and hit the server very hard if you were to choose OME-TIFF format). But if it is useful to you, I can provide you with an updated script that you can install to allow you to do this (without waiting for the next OMERO release)?

Many thanks for your feedback.

Regards,

Will & Petr

Hi Will and Petr,

Thanks for addressing all my questions and sorry for my late response (distracted by other stuff). I will get to installing V 5.0 as soon as I find the time. Meanwhile, having a version of the Batch Image Export script that DOES export a whole Plate would be great. Thanks if you find the time to whip that up.

Cheers,
- Damir