[ome-users] Retrieving original images from the server

[Curtis Rueden]

Hi,

> Note: ImageJ fundamentally sees images as 2D structures, while we
> fundamentally see them as 5D-- this gives us some serious gymnastics
> to deal with.  Bear with us.

Recently, ImageJ added support for "hypervolumes," which are 5D much
like OME is. This construct will make the mapping between ImageJ and
OME a lot more straightforward, although Jason is still right that
there are some gymnastics to handle certain types of functionality,
such as retrieving image planes from the server on demand rather than
pulling down an entire 5D pixels block at once.

-Curtis

On Dec 4, 2007 5:50 PM, Jason Swedlow <jason at lifesci.dundee.ac.uk> wrote:
> Hi Paulo-
>
> On 29 Nov 2007, at 12:52, Paulo Almeida wrote:
>
> > Hi Jason and Curtis, thanks for your replies.
> >
> >>> We have plans to update the "Upload to OME" plugin to work with
> >>> OMERO,
> >>> but have not yet had time to do so. It is definitely something we
> >>> will
> >>> add in the future, though.
> >>
> >> We'd appreciate feedback on this point-- is this a major priority for
> >> the community?  We know ImageJ is in heavy use, and therefore are
> >> considering devoting resources to this.  Does the ImageJ community
> >> want this?
> >
> > ImageJ/OMERO integration is important for our community, because we
> > want to
> > minimize the number of applications people need in order to use
> > OMERO. My
> > idea is to have OMERO.importer installed in the microscope
> > computers and a
> > client (Insight and/or ImageJ) on the researcher's computers. Since
> > they are
> > already using ImageJ to further process their images, it would be
> > good if
> > they could just import them from the database within ImageJ.
>
> Obviously, I was asking a leading question.  We are currently working
> to provide the first tools for running analyses in OMERO, with the
> ultimate aim of providing interfaces for MatLab, R, ImageJ,
> CellProfiler, and any other system that can communicate via java, C++
> or Python.  We have been moving forward towards this in steps for
> some time.  There is alot to do here, so will take a few more months.
> The first parts of this should be available in Beta3.  For more info,
> see:
>
> http://trac.openmicroscopy.org.uk/omero/ticket/846
>
> Note: ImageJ fundamentally sees images as 2D structures, while we
> fundamentally see them as 5D-- this gives us some serious gymnastics
> to deal with.  Bear with us.
>
> >
> > Ideally, OMERO.importer could have basic annotation capabilities,
> > because
> > people have been saying they have limited time on the microscopes,
> > so they
> > will end up writing something on their notebook instead of using
> > OMERO.insight while they are acquiring images. Sometimes
> > acquisition takes up
> > to a minute and that is the time they use to annotate, and of
> > course the
> > image is still not available in Insight. Actually, it is not
> > available in
> > Importer too, at that stage, so they would probably write something in
> > Notepad and paste it to Insight afterwards, but if they could paste
> > it to
> > Importer instead, they would just need to use one program. What do
> > you think?
>
> I think it is great!!!!
>
> We are doing alot of foundation work around the import engine now,
> and will discuss working that in.
>
> Cheers,
>
> Jason
>
>
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