[ome-users] splitting a multi-image series

Fri Jun 5 16:03:41 BST 2015

Damir,

I meant Aperio ImageScope, sorry ;-)

Kind regards
Ola

From: Damir Sudar <dsudar at lbl.gov<mailto:dsudar at lbl.gov>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Fri, 5 Jun 2015 16:25:46 +0200
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] splitting a multi-image series

Thanks Ola, this is the OpenSlide software on: http://openslide.org/ , right? I'll definitely look at that. And yes, I already suggested that they look at ways to omit the label and thumbnail while scanning. I'm myself also not familiar with the Aperio scanner software but they are.
Cheers,
- Damir

On Fri, Jun 5, 2015 at 3:32 PM, Aleksandra Tarkowska (Staff) <A.Tarkowska at dundee.ac.uk<mailto:A.Tarkowska at dundee.ac.uk>> wrote:
Hi Damir,

It was nice to meet you in Paris.

We used Aperio software called OpenSlide to permanently remove label from raw data as making it invisible in OMERO is not enough (remember about download button).
I personally have never scanned slides but I am pretty sure there should be an option to choose not to scan label and/or thumbnail.

Kind regards
Ola

From: Damir Sudar <dsudar at lbl.gov<mailto:dsudar at lbl.gov>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Fri, 5 Jun 2015 13:36:31 +0200
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] splitting a multi-image series

Thanks Petr. I've forwarded your suggestion to my user and let him decide whether that approach is adequate for him or not. I agree that covering the label-part of the slide before scanning is the most appropriate thing to do.
- Damir

On Fri, Jun 5, 2015 at 1:27 PM, Petr Walczysko (Staff) <p.walczysko at dundee.ac.uk<mailto:p.walczysko at dundee.ac.uk>> wrote:
Hi Damir

Thank you very much for your feedback.
You are right, the Move action will not help you in the workflow you are describing, OMERO always forces you to Move the whole component into the different group,
so I would not go this way anymore.

The best workflow I have for hiding parts of mulit-image series is to

  - create a new dataset  (e.g. named "dump")
  - use in Web or Insight the Cut and Paste (right-click context menu) on the images with labels to remove them from the vicinity of the other, valuable (or unlabelled) multi-image series
  - Paste the images into the "dump" dataset

I realise now that this might not be sufficient enough for your user, because probably a full covering/removal of the labelled images is asked for (in my workflow above, the labelled images will
STILL be visible and accessible when you expand and browse the "dump" folder ) but I am not aware of any better workflow at the moment, possibly one of my colleagues might come up with
some better answer yet.

All the best

Petr

Petr Walczysko
OME Team

On 5 Jun 2015, at 10:35, Damir Sudar <dsudar at lbl.gov<mailto:dsudar at lbl.gov>> wrote:

Hi OME team,

Thanks for an extremely useful and fun User's Meeting this week.

During one of the sessions I had asked whether there was any way to remove one of the components of a multi-image series (one of my users is uploading Aperio .svs images and would like to remove the image of the label because of concerns of it having identifiable patient info on it). Anyway, in your answer it was very clear that actually removing is impossible since all components are in the same image file in the repo so I completely understand that. However, I think it was Josh who suggested that it may be possible to make one of the components not visible and I thought I had remembered that one could do so by moving that component to a different group. I just tried and OMERO tells me very clearly that all components must stay together in the same group. Was there some other way to make one component of a multi-image series not visible?

I already suggested to the user that he could simply obscure the label before scanning but alas, they have scanned ~1000 slides already .....

Thanks,
- Damir

--
Damir Sudar - Staff Scientist
Lawrence Berkeley Laboratory / Life Sciences Division
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346<tel:510%2F486-5346> - F: 510/486-5586<tel:510%2F486-5586> - E: DSudar at lbl.gov<mailto:DSudar at lbl.gov>

Visiting Scientist, Oregon Health and Science University
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--
Damir Sudar - Staff Scientist
Lawrence Berkeley Laboratory / Life Sciences Division
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346<tel:510%2F486-5346> - F: 510/486-5586<tel:510%2F486-5586> - E: DSudar at lbl.gov<mailto:DSudar at lbl.gov>

Visiting Scientist, Oregon Health and Science University
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The University of Dundee is a registered Scottish Charity, No: SC015096

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ome-users mailing list
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--
Damir Sudar - Staff Scientist
Lawrence Berkeley Laboratory / Life Sciences Division
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov<mailto:DSudar at lbl.gov>

Visiting Scientist, Oregon Health and Science University
_______________________________________________ ome-users mailing list ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
The University of Dundee is a registered Scottish Charity, No: SC015096
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