[ome-users] OMERO.figure release 1.0.0
William Moore
will at lifesci.dundee.ac.uk
Wed Oct 29 23:15:59 GMT 2014
Hi Christophe,
You can choose images by copying and pasting the "image link" as shown in the first video
on this page:
http://will-moore.github.io/figure/videos.html
If you have the PDF figures attached to the images (and these contain a link to the Figure url),
do you still need the figure itself to be attached to the images?
Since the figure file (json) attachment doesn't give you any way to re-open the figure in OMERO.figure (no link).
Please use github issues at https://github.com/will-moore/figure/issues for feature requests, bugs etc.
Thanks for the feedback,
Will.
On 29 Oct 2014, at 17:43, Christophe TREFOIS <christophe.trefois at uni.lu> wrote:
> Hi Will,
>
> Thanks for the extensive answer.
>
> Also, I wanted to congratulate you on the plugin. It gets a fantastic acceptance from our users. They love it!
>
> Hopefully in a next version, choosing images can be simplified, as writing down the IDs works but is a bit cumbersome.
>
> We will re-enable the saving option, as people were a little bit clueless where to find the actual figure. For them it belongs to the context of the image, but as you explained there is nothing to be found, so a bit confusing.
>
> Another aspect is that if you have many figures, it becomes difficult to find back the figure you want. However, opening the attachment from an image and then going straight to that figure seems much more logical in such a workflow.
>
> P.s.: Should feature requests be made on github or on another OME server?
>
> Kind Regards,
>
> --
> Christophe
>
> From: William Moore [mailto:will at lifesci.dundee.ac.uk]
> Sent: jeudi 9 octobre 2014 15:23
> To: Christophe TREFOIS; ome-users at lists.openmicroscopy.org.uk Users
> Subject: Re: [ome-users] OMERO.figure release 1.0.0
>
> Hi,
>
> Are you already making images "public" via the OMERO.web public user as described https://www.openmicroscopy.org/site/support/omero5/developers/Web/PublicData.html ?
>
> In general I have tried to make the OMERO.figure files adopt the same permissions (same group) as the
> images that are used in each figure. So, by default the figure should start out with the same permissions as it's images.
> (It's actually possible to combine images from different groups into a single figure, but I'm assuming most users don't do this).
>
> However, we don't currently attach the figure to any of the images that are in the figure.
> So, if you choose to move those images to a "public" group, the figure file will remain in it's original group.
>
> If you want to also move the figure file to the "public" group, the only way to do this is to attach it to
> one of the images that are in the figure, then move that image to the public group.
> You can attach the figure by clicking the Attachments [+] button in the image right panel, then browsing existing files
> on OMERO and picking the figure by name.
>
> This should cause the figure file to move to that group too.
> Then, you should only need to allow the public user to access "figure" urls (by configuring the public url filter - see docs link above)
> and it should just work.
> I haven't actually tested this complete workflow, but it should be fine.
>
> NB: Just before the OMERO.figure 1.0.0 release, I added code that attached the figure file to all the
> images in the figure each time you Saved the figure. However, I disabled this for the release, since
> it made it too easy to accidentally delete the figure file when looking at the image in web-client.
> See https://github.com/will-moore/figure/issues/21#issuecomment-57457959
>
> If you want to enable this, you can simply set LINK_TO_IMAGES = True in figure/views.py
> https://github.com/will-moore/figure/blob/develop/views.py#L244
>
> In future versions of web-client, we'll make it harder to delete figure files, then we can re-enable this linking on save.
>
> Hope that helps,
>
> Will.
>
>
>
> On 8 Oct 2014, at 17:11, Christophe TREFOIS <christophe.trefois at uni.lu> wrote:
>
>
> Also, sorry to bug you more, but how would you change permissions on a « figure » object?
>
> Eg, say I have the following workflow
>
> 1. Create figure with user: toto
> 2. Finish figure that goes to publication
> 3. Want to make figure public to everyone can “interact” with it
>
> I couldn’t find that in your documentation, maybe I’m blind L
>
> Cheers and kudos for this awesome toolü
>
> From: Christophe TREFOIS
> Sent: mercredi 8 octobre 2014 17:59
> To: 'William Moore'
> Subject: RE: [ome-users] OMERO.figure release 1.0.0
>
> Sweet !
>
> Do you know of any efforts to have the whole OMERO in this beautiful typset ?
>
> Also, I opened some issues on git for figure1.0.0, I hope that’s the place you expect feedback.
>
> Best!
>
> From: William Moore [mailto:will at lifesci.dundee.ac.uk]
> Sent: mercredi 8 octobre 2014 15:49
> To: Christophe TREFOIS
> Subject: Re: [ome-users] OMERO.figure release 1.0.0
>
> Hi,
>
> Yes, exactly. Twitter bootstrap makes everything easy!
>
> Also using Raphael.js for rectangles on selected panels and backbone.js for everything else.
>
> Cheers,
>
> Will.
>
>
>
> On 8 Oct 2014, at 14:45, Christophe TREFOIS <christophe.trefois at uni.lu> wrote:
>
>
> Hi Will,
>
> Sorry I will just bluntly ask like this, but how do you get your OMERO to look so pretty ? (I’m guessing Twitter Bootstrap 3?)
>
> Any pointers would be so welcome J
>
> Best,
>
> P.s.: Installing OMERO.figure now…
>
> From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of William Moore
> Sent: lundi 6 octobre 2014 16:58
> To: ome-users at lists.openmicroscopy.org.uk Users
> Subject: [ome-users] OMERO.figure release 1.0.0
>
> Hi All,
>
> Today we have released OMERO.figure 1.0.0, which includes support for Z-projections.
>
> To see the full release announcement, go to http://will-moore.github.io/figure/2014/10/06/release-1.0.0.html
>
>
> A video of the new features is at https://www.youtube.com/watch?v=P0MMKtIKdFY
>
> And there are more tutorial videos at http://will-moore.github.io/figure/videos.html
>
>
> If you haven't tried OMERO.figure yet, you can read more and experiment with the demos listed on the
> recently updated home page: http://will-moore.github.io/figure/
>
>
> Regards,
>
> Will.
>
>
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