[ome-users] OMERO import - txt format

[Andrea Falconi]

Hello Olaf,

In a nutshell, I don't think there's an out-of-the box solution that would
be a good fit for your use case---I obviously stand to be corrected. But if
you're willing to roll up your sleeves and write some code you could try
one of the approaches below.

> is there any existing solution that allows batch import and/or GUI-based
import with „in-place“ import?
Not that I'm aware of. But I think it shouldn't be too difficult to put
together a front-end web page that collects import input and then spawns a
process to run the CLI to do an in-place import as documented here:

* https://docs.openmicroscopy.org/omero/5.4.1/sysadmins/in-place-import.html

Note that you'll need to set up a suitable environment for this to
happen---read the instructions carefully ;-)

> Does Smuggler do „in-place“ import too
Not at the moment, but it could be implemented relatively easily---I
welcome contributions :-)
As an added benefit, you could then use this modified version OMERO.Insight:

* https://github.com/MontpellierRessourcesImagerie/openmicroscopy/releases

which uses Smuggler's REST API to do offline imports. This is the version
we're currently using at the CNRS in Montpellier to let our users import
files into OMERO.
Like I said both approaches involve writing some code. If you want to do
that I'll gladly help you out in whichever way I can.

Kind regards

/a





On 6 December 2017 at 14:06, <microscopy at olafselchow.de> wrote:

> Dear list,
>
> Sorry .. previous post was strangely html-formatted ... this one should be
> readable:
>
> I am struggeling a bit with understanding the various ways of OMERO
> import. Maybe someone can clarify:
>
> We want to implement a workflow for importing image data (mostly from
> Nikon instruments) into OMERO (5.x) using the in-place import
> functionality. Copy/Transfer of the data is no option due to the sheer
> amount of data.
> The storage volume where the data sits is a network drive mounted to the
> OMERO.server (> 100 TB, likely to be extended soon).
>
> Now: is there any existing solution that allows batch import and/or
> GUI-based import with „in-place“ import? Command-line operation is not
> acceptable by the user.
> Does Smuggler do „in-place“ import too? (couldn’t find any comment on this
> on the smuggler description page)
> Anyone out there who has built something on Atom (
> https://www.medfloss.org/node/695[https://deref-web-02.
> de/mail/client/e4_FB63n2yQ/dereferrer/?redirectUrl=https%
> 3A%2F%2Fwww.medfloss.org%2Fnode%2F695]) to make it work with OMERO 5.x
> and extend to „in-place“?
>
> As a starting point, I would like to get an overview on what is already
> available. (—> Is https://www.openmicroscopy.org/omero/import/[https://
> deref-web-02.de/mail/client/GduavfPOucg/dereferrer/?
> redirectUrl=https%3A%2F%2Fwww.openmicroscopy.org%2Fomero%2Fimport%2F] a
> comprehensive list?)
>
> Thanks a lot!
> Olaf
>
> ———
> Olaf Selchow
> Microscopy & BioImaging Consulting
> microscopy at olafselchow.de
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20171206/0e243344/attachment.html>