[ome-devel] exporting images from old version of OMERO

[Phil Chapman]

Thanks for the response Josh.

I too concluded that Omero.Py would probably allow me to do what I want -
i.e. To export programatically to a linux environment.  I just wanted to
make sure that there was nothing server-side that would have to be set up?
 Will the client-side python api work even though the server-side batch
export python script doesn¹t work?

I have spent some time today trying to install OMERO.py 4.4.11.10 with
limited success, mainly due to issues installing an old version of ICE
(v3.3).  I thought I might be able to set up a portable environment using
Docker but I think I reached the limit of my linux sys admin skills.

I think you¹re right that I should contact Perkin-Elmer to see what they
have to say first - there¹s no immediate urgency to this.  If I don¹t get
anywhere I¹ll be sure to get in touch with Glencoe.

Thanks.

On 03/10/2016, 15:40, "ome-devel on behalf of Josh Moore"
<ome-devel-bounces at lists.openmicroscopy.org.uk on behalf of
josh at glencoesoftware.com> wrote:

>On Fri, Sep 30, 2016 at 11:57 AM, Phil Chapman
><Phil.Chapman at cruk.manchester.ac.uk> wrote:
>> Hi,
>
>Hi Phil,
>
>
>> Our institute has the commercial Columbus software which happens to use
>>OMERO 4.4.11.10 as its image repository, and for this reason I was
>>hoping that this group might be able to help.
>
>a quick response from our side though suggestions from the community
>are welcome.
>
>
>> We are in the process of generating a large compound screening dataset
>>(in the region of 100 384-well plates) and to analyse this data we want
>>to make use of our 1000-core linux cluster that we typically use for NGS
>>analysis rather than the 32 core cluster that Columbus is hosted on (we
>>have estimated that analysing our dataset would take 3 days on this!!).
>>I have done some test exports from Columbus into the OME-TIFF format
>>(using Columbus Helper), and have analysed data using the R EBImage
>>package and this all works just fine.  However, since Columbus Helper is
>>only available for Windows and Mac, I want to develop a programmatic way
>>to do this transfer straight to the linux cluster.
>
>You're primarily interested in the binary image data? If so,
>`bin/omero export` may be a starting point in OMERO 4.4:
>
>
>https://github.com/openmicroscopy/openmicroscopy/blob/v.4.4.11/components/
>tools/OmeroPy/src/omero/plugins/export.py
>
>which exports on an image-by-image basis. (There have been a number of
>file leakage fixes since 4.4 which may or may not pertain. Keep an eye
>on the open file handles for the server).
>
>
>> I can connect to the OMERO repository just fine with OMERO.insight and
>>view the data structure and see images, but the batch export
>>functionality and any processing or exporting doesn¹t work because it
>>can¹t find a processor to use ­ presumably it¹s set up in such a way
>>that OMERO only stores images rather than processes them?
>
>This sounds like the "export and zip together" functionality for a
>whole plate. Likely you don't particularly need the functionality of
>batch exporting when working from a cluster (nor want the added burden
>of storing the zips).
>
>
>> Does anyone have any suggestions given that this is quite an old
>>version of OMERO, and that the OMERO server doesn¹t seem to have any
>>compute resources.  If someone could point me in the right direction
>>then that would help greatly!  I¹m hoping there¹s some sort of Python or
>>Java API I can make use of maybe?
>
>This is probably as far as we can go in supporting OMERO 4.4 on the
>mailing lists. In addition, you may want to contact PerkinElmer
>support before trying anything too significant. If you continue to
>have issues, though, you're welcome to contact
>info at glencoesoftware.com about dedicated support.
>
>
>> Thanks in advance,
>>
>> Phil Chapman
>
>All the best,
>~Josh.
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