[ome-users] ome-users Digest, Vol 115, Issue 17

Wed Oct 29 21:12:07 GMT 2014

Hi Connor,

OK, I definitely have a problem with the timing of the Andor cameras in MetaMorph.  Attached are an 8-bit version of a snapped image and a screen shot of the live image for the same settings.  There is very clearly vibration in the snapped image, which I assume is the shutter.  I see this with both the sCMOS and the EM-CCD on the confocal side.

There are other behaviors pointing to a shutter/camera timing issue:
1. If I set the trans shutter to be always open, the snapped image looks the same as the live image.

2. If I change the hardware setting for the transmitted light shutter in MetaMorph to an "open delay" of 1 second, there isn't any change in the amount of time it takes to snap a 100ms exposure (and it is definitely shorter than 1 second).  With a 1 second delay, as opposed to the normal 20ms delay, I would expect a noticeable difference in total time from command to image for a 100ms exposure.

3. I do not see this vibration with the iQ software--the Live and Snap images look the same.

Please let me know when you will have some time to work with me on this.

I am running MM 7.8.2 and iQ 2.2.1 on Win7 32-bit. 

Many thanks,
Wendy

~~~~~~~~~~~~~~~~~~~~~~~
Wendy Salmon
Light Microscopy Specialist
Whitehead Institute for Biomedical Research
W.M. Keck Imaging Facility
9 Cambridge Center, Rm 447
Cambridge, MA 02142
c: 617-429-0158
e: wsalmon at wi.mit.edu
w: http://staffa.wi.mit.edu/microscopy/

----- Original Message -----
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To: ome-users at lists.openmicroscopy.org.uk
Sent: Wednesday, October 29, 2014 2:08:58 PM
Subject: ome-users Digest, Vol 115, Issue 17

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Today's Topics:

   1. Re: PixelData errors (Josh Moore)
   2. OMERO sub-folders (Christophe TREFOIS)
   3. Re: OMERO.figure release 1.0.0 (Christophe TREFOIS)
   4. Re: OMERO sub-folders (Douglas Russell)

----------------------------------------------------------------------

Message: 1
Date: Wed, 29 Oct 2014 14:26:54 +0100
From: Josh Moore <josh at glencoesoftware.com>
To: "Tjelvar Olsson (JIC)" <Tjelvar.Olsson at jic.ac.uk>
Cc: "ome-users at lists.openmicroscopy.org.uk"
	<ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] PixelData errors
Message-ID: <22E05792-9FB0-4588-A53F-58B1CC00FD7E at glencoesoftware.com>
Content-Type: text/plain; charset=us-ascii

On Oct 28, 2014, at 1:27 PM, Tjelvar Olsson (JIC) wrote:

> Dear all,

Hi Tjelvar,

> I have been working on creating an ansible script for automating the
> installation of an OMERO server on Centos 6.5.
> 
> The ansible script seems to be working and I can create a clean
> installation from scratch.

Interesting! Let us know how that goes.

> However, when I run the diagnostic tool on a clean install I get a
> number of warnings and some errors.
> Log files:  PixelData-0.log                18.0 KB       errors=7
> 
> My question is: should I be worried about the PixelData errors (log file
> attached)?
> What do they mean and why are they raised?
> 
> Example error:
> 
> org.springframework.dao.DuplicateKeyException:
> PreparedStatementCallback; SQL [insert into configuration (name, value)
> values (?,?)]; ERROR: duplicate key value violates unique constraint
> "configuration_pkey"; nested exception is
> org.postgresql.util.PSQLException: ERROR: duplicate key value violates
> unique constraint "configuration_pkey"

Yes, this is a problem that's popped up a few times. See
http://trac.openmicroscopy.org.uk/ome/ticket/10181

Unfortunately, we haven't worked out a fix yet. Running the
following should restart the service and the bottom of the log
should look happier:

  bin/omero admin ice server stop PixelData-0

> Kind regards,
> Tjelvar

Cheers,
~Josh

------------------------------

Message: 2
Date: Wed, 29 Oct 2014 17:35:08 +0000
From: Christophe TREFOIS <christophe.trefois at uni.lu>
To: "ome-users at lists.openmicroscopy.org.uk"
	<ome-users at lists.openmicroscopy.org.uk>
Subject: [ome-users] OMERO sub-folders
Message-ID: <2EBB29CB9A8F494FB5253F6AF2E6A1981C658BA9 at hoshi.uni.lux>
Content-Type: text/plain; charset="iso-8859-1"

Dear all,

Is there a specific reasoning as to why it is not possible to create multiple sub-folders to sort images in ?

My understanding is that together with OMERO.webtagging a rather complex structure can be created where users can search for and find their images. However, traditionally, users are used to store their images in multiple sub-folders.

Perhaps somebody could elaborate a bit and thus enlighten our staff? :)

Thanks,

................................................................................

Dr. Christophe TREFOIS, Dipl.-Ing.
Doctor in Biology
Senior Technical Specialist

UNIVERSIT? DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE

Campus Belval | House of Biomedicine

7, avenue des Hauts-Fourneaux

L-4362 Esch-sur-Alzette

T +352 46 66 44 6124
F +352 46 66 44 6949
www.uni.lu/lcsb<http://www.uni.lu/lcsb>

This message is confidential and may contain privileged information.
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Message: 3
Date: Wed, 29 Oct 2014 17:43:28 +0000
From: Christophe TREFOIS <christophe.trefois at uni.lu>
To: William Moore <will at lifesci.dundee.ac.uk>,
	"ome-users at lists.openmicroscopy.org.uk Users"
	<ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] OMERO.figure release 1.0.0
Message-ID: <2EBB29CB9A8F494FB5253F6AF2E6A1981C658BCD at hoshi.uni.lux>
Content-Type: text/plain; charset="iso-8859-1"

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<mailto: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 :(

Cheers and kudos for this awesome tool?

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<mailto: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 :)

Best,

P.s.: Installing OMERO.figure now...

From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk<mailto: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<mailto: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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Message: 4
Date: Wed, 29 Oct 2014 18:08:36 +0000
From: Douglas Russell <douglas.russell at bioch.ox.ac.uk>
To: Christophe TREFOIS <christophe.trefois at uni.lu>
Cc: "ome-users at lists.openmicroscopy.org.uk"
	<ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] OMERO sub-folders
Message-ID:
	<CAE9O58C9mpL=QcK0uGtBwC1ut0ehNHkcrntXzj9AEDiyR6p_1w at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Christophe,

Indeed this is a much desired feature! In the simplest possible terms, the
reason we do not have sub-folders is because it is hard to do this well in
a database especially once you consider permissions, in the filesystem, if
it's above you, it is the master of you. This is not so in a database.

However, I'm encouraged to find that you have discovered OMERO.webtagging.
Yes, it can be used to similar (and I believe in many ways, superior)
effect than infinitely nested hierarchies. The tagsearch feature is a very
simple implementation of a visualisation of the tag structure you have
created. I have plans to implement a tree-like view of the tagged data, but
this was stalled somewhat while I have upgraded many components of
OMERO.web to support this work. I hope to return to it at the end of the
year.

The idea is to display a tree-like structure that is familiar to the users,
but is in fact working similar to tagsearch, refining the search results
each time the user 'navigates' into a 'directory'. This functionality will
come with a serious caveat, which is that it will not scale to huge amounts
of data/tags because the queries will start to run very slowly because of
how the tags are stored in the system. I hope to create this proof of
concept to show that tags are powerful and useful with the idea that
utilising new technology in OMERO in the future, (e.g. graph databases) we
are able to scale this up.

Thanks,

Douglas

On 29 October 2014 17:35, Christophe TREFOIS <christophe.trefois at uni.lu>
wrote:

>  Dear all,
>
>
>
> Is there a specific reasoning as to why it is not possible to create
> multiple sub-folders to sort images in ?
>
>
>
> My understanding is that together with OMERO.webtagging a rather complex
> structure can be created where users can search for and find their images.
> However, traditionally, users are used to store their images in multiple
> sub-folders.
>
>
>
> Perhaps somebody could elaborate a bit and thus enlighten our staff? J
>
>
>
> Thanks,
>
>
>
>
> *................................................................................*
>
> *Dr. Christophe TREFOIS, **Dipl.-Ing.*
> *Doctor in Biology*
>
> Senior Technical Specialist
>
> UNIVERSIT? DU LUXEMBOURG
>
>
>
> LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
>
> Campus Belval | House of Biomedicine
>
> 7, avenue des Hauts-Fourneaux
>
> L-4362 Esch-sur-Alzette
>
> T +352 46 66 44 6124
> F +352 46 66 44 6949
> www.uni.lu/lcsb
>
>
>
> *This message is confidential and may contain privileged information. *
>
> *It is intended for the named recipient only. *
>
> *If you receive it in error please notify me and permanently delete the
> original message and any copies.*
>
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
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