Open Microscopy Environment

Hi,

we are running Omero 5.0.0 on a Linux machine in a multi-client environment and some of our users requested to be able to mass export the original format of their uploaded images (currently via OMERO Dropbox). As far as I could find out, currently only OMERO-TIFFs can be exported, but the feature is being worked on.

For us this feature would be crucial since a lot of experimenters are used to work with their standard image analysis tools supplied by the microscope vendors.

Regards,

Tristan

Hi Tristan

OMERO 5 allows you to download your original file. For example, in the web select an image, click in the down arrow in the right-hand pane (the tooltip will say "Download image as ..."), and choose "Archived file".

If you were referring to the "Batch Image Export" script then it doesn't currently support exporting the original files, is this what you meant?

Simon

Hi Simon,

thanks for your reply. I tried using the download button in OMERO.Web earlier, but all it gives me is OME-TIFF and JPEG ("Archived file" is not shown), although the image I am trying to download is a Zeiss czi file.

I found out, however, that OMEOR.insight is able to handle multiple downloads to some chosen location and also allows you to download the original files. To make this work on OMERO-Web:

a) Do we have to change any server settings or settings in OMERO-Web to get this option?

b) I guess from your answer (and the documentation) that "Batch Image Export" is what a user should use for mass downloading files in OMERO.Web. Is there any way to get this working with original files? This is exactly what our users need, since downloading file by file is inconvenient and not an option for very large data sets.

Thanks,

Tristan

PS: When I select multiple CZI files in OMERO.insight, I can choose "Download" by clicking the red down arrow on the right pane to download all original files or I can choose Save as JPEG/PNG/TIFF, but Export as OME-TIFF is greyed out.

Using Save as -> TIFF will not give you OME-TIFFs (as it seems), since it produces a ZIP archive containing single images for every image in a time series (previously stacked in the CZI file) and I thought OME-TIFFs support image stacks.

Is there any option to mass download OME-TIFFs just as easy as the original files by using OMERO.insight?

Hi Tristan,

Hmmm - it seems like there's a bug in OMERO.web - it should always give you the option to download the original file. I'll create a ticket to look at that ASAP. https://trac.openmicroscopy.org.uk/ome/ticket/12136

I can also look at adding the "Original file" option to the Batch Image Export script.
https://trac.openmicroscopy.org.uk/ome/ticket/12137

Cheers,

Will.