[ome-users] splitting a multi-image series

Fri Jun 5 16:18:16 BST 2015

Perfect, thanks!!
- Damir

On Fri, Jun 5, 2015 at 5:06 PM, Aleksandra Tarkowska (Staff) <
A.Tarkowska at dundee.ac.uk> wrote:

>   You can download it for free
> http://www.leicabiosystems.com/pathology-imaging/aperio-digital-pathology/integrate/epathology-imagescope/
>
>  Kind regards
> Ola
>
>   From: Aleksandra Tarkowska <a.tarkowska at dundee.ac.uk>
> Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
> Date: Fri, 5 Jun 2015 15:03:41 +0000
> To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] splitting a multi-image series
>
>   Damir,
>
>  I meant Aperio ImageScope, sorry ;-)
>
>
>  Kind regards
> Ola
>
>   From: Damir Sudar <dsudar at lbl.gov>
> Reply-To: OME User Support List <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>
> 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> 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>
>> Reply-To: OME User Support List <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>
>> 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> 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> 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 - F: 510/486-5586 - E: DSudar at lbl.gov
>>>
>>>  Visiting Scientist, Oregon Health and Science University
>>>    _______________________________________________
>>> ome-users mailing list
>>> 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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>>>
>>
>>
>>  --
>>    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
>>
>>  Visiting Scientist, Oregon Health and Science University
>>    _______________________________________________ ome-users mailing
>> list 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
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>
>
>  --
>    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
>
>  Visiting Scientist, Oregon Health and Science University
>    _______________________________________________ ome-users mailing list
> 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
>  _______________________________________________ ome-users mailing list
> 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
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>

-- 
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

Visiting Scientist, Oregon Health and Science University
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