[ome-users] Orbit Image Analysis v2.41

[Jason Swedlow (Staff)]

Hi Manuel-

Thanks for the updates and all the great work.  It's great to see this going forward.

We have a very cool IPS cell project going on in the lab and was very excited to use Orbit to work through some analyses on some of the data collected by a few of my colleagues.  I ran into the same problem as Damir- I couldn't access data owned by other members of my group (in an OMERO sense).  Speaking selfishly, this is a really important capability- did I miss something, or can this be added?

Thanks again for all the great work.

Cheers,

Jason

From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of Damir Sudar <dsudar at lbl.gov<mailto:dsudar at lbl.gov>>
Reply-To: OME Users <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Tuesday, 8 November 2016 06:22
To: OME Users <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] Orbit Image Analysis v2.41

Hi Manuel,
Orbit is a very impressive piece of software and it looks like it will be very useful for a number of projects at our institute. I look forward to spending some time getting familiar with it.
I noticed a few things I wanted to ask you about:
1) i saw that ROI annotations are saved on the OMERO server as small attachment files in a format that is not easily parsed. Do you have any plans to store those ROIs as OMERO ROIs so they can be handled using the other OME tools and associated software? Or is there a way to decode the Orbit Annotations so they can be converted to OMERO ROIs (and vice versa)?
2) when connecting with an OMERO server, you get the directory of files in the user's default group. Is there a way to select a different group for those users that are a member of multiple OMERO groups?
Thanks,
Damir

Sent from my iPad, please excuse poor spelling

On Nov 7, 2016, at 06:54, Manuel Stritt <manuel.stritt at actelion.com<mailto:manuel.stritt at actelion.com>> wrote:


Hello together,

I just released the new Orbit version which allows you to open and work with whole slide images directly from local file system, even without an image server.
(However, the preferred method will always to to connect to an image server like Omero.)

This is the outcome of the feedback from many of you who wanted to work with local files (e.g. SVS, NDPI, SCN, ...) directly without the need of
installing an image server first.

This has been made possible by using the Scifio/Bioformats library form OME (we use version 5.2.4), so a big thanks goes out to the Bioformats team.

In addition to this some performance improvements have been implemented (much faster rendering) and some bugs have been fixed.
See here<http://www.orbit.bio/2016/11/07/open-local-images/> for more details and give it a try!

I also added more tutorials (under documentation).

http://www.orbit.bio/

Kind Regards,
Manuel


--
Manuel Stritt
Information Management Drug Discovery



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