[ome-users] Super-resolution data in OMERO

Mon Sep 15 19:06:51 BST 2014

Dear All

The majority of those who have expressed interest in  a meeting seem to be based either in London or Oxford.
What do people think  about a physical venue in the South-East of England and virtual attendance for the others?

Hopefully the OME team in Dundee can advise on the virtual part,  as their setup seems to work well.

All the best

Ian

On 15 Sep 2014, at 10:00, Keller, Debora <d.keller at imperial.ac.uk<mailto:d.keller at imperial.ac.uk>> wrote:

Hello!

Happy to join a meeting wherever that may take place!
Best wishes,

Debora

Debora Keller, PhD

FILM - Facility for Imaging by Light Microscopy
- Super-Resolution Microscopy Specialist -
Sir Alexander Fleming Building, desk 408
Imperial College London / South Kensington
Exhibition Road
London SW7 2AZ, UK
Phone: +44 (0)207 594 9793
Mobile: + 44(0) 7760 256 889
E-mail:  d.keller at imperial.ac.uk<mailto:d.keller at imperial.ac.uk>
Website: http://imperial.ac.uk/imagingfacility

From: Ashley J Cadby [mailto:a.cadby at sheffield.ac.uk]
Sent: 14 September 2014 16:22
To: Jason Swedlow
Cc: Ricardo Henriques; Kwakwa, Kwasi A; French, Paul (PHOT) M W (Photonics); Douglas Russell; David Pinto; Joshua Moore; Munro, Ian; Jean-Marie Burel; Ilan Davis; Simon Li; Dunsby, Christopher W; Keller, Debora; Pedro Almada; Nils Gustafsson; Sian Culley
Subject: Re: Super-resolution data in OMERO

Dear all
I think this would be a great event. I am happy to host it in Sheffield if people want a half way destination between London and Dundee.
Ash

Sent from my iPhone

On 14 Sep 2014, at 14:08, Jason Swedlow <j.r.swedlow at dundee.ac.uk<mailto:j.r.swedlow at dundee.ac.uk>> wrote:

Dear All

Thanks to Paul for initiating this discussion and to the rest of you for taking it forward.  A few thoughts--

1. It would be great if we could move this over to the OME developers mailing list, as I think several others would be interested in at least knowing about this and probably participating.

2.  Simon Li has previous emails to that list discussing a Features API concept (I'm on a mobile device so a bit tricky to find the archived email, but shouldn't be too hard to search the archives).  If I understand the reqs of what we are discussing here, his concepts should align nicely, especially with what Ricardo suggested in the last email in this thread.

3. If we can decide what we want to do, would be great to hold a development meeting (hackathon, etc).  London, Oxford/or Dundee would be fine. That shouldn't be too hard to organise.

4.  In OME, we've become pretty wedded to a development process that includes a lot of testing and QA.  Having real users inform us of what we need to do, and then capturing those reqs in tests would be hugely helpful, and at least for us, mandatory for making a production release. If we have those, terrific.  If we don't, does anyone know how to get them?

Thanks again to all.  This is great!

Cheers,

Jason

Centre for Gene Regulation & Expression | Open Microscopy Environment | University of Dundee

On Sat, Sep 13, 2014 at 1:59 pm, Ricardo Henriques <r.henriques at ucl.ac.uk<mailto:r.henriques at ucl.ac.uk>> wrote:

Dear Kwasi,

I think this would be a very good idea. I'm adding a few more people to the thread that might be interested.

Shall we setup a meeting?

>From discussions with Debora and bit of googling we got the idea that it would be fairly feasible to create a python script for OMERO that calls the PALM/STORM image analysis software either in the client or server side. I have a couple of ideas of what could be used, for example:
- its easy to call ImageJ running QuickPALM as a python subprocess, the same perhaps for ThunderSTORM
- DAOSTORM already features a Python interface that can be adapted into an OMERO Python script.

I'm happy to donate code on my side whenever possible.

All the best,
-Ricardo

On Fri, Sep 12, 2014 at 1:03 PM, Kwasi Amoako Kwakwa <k.kwakwa at imperial.ac.uk<mailto:k.kwakwa at imperial.ac.uk>> wrote:
Hello All,

I spoke to Debora Keller and Ricardo Henriques about integrating OMERO more
closely with localization microscopy analysis and visualization tools and they
both seemed really interested, plus I think they might be aware of other
people looking for something similar. It looks like we are going to end up
with a decent-sized group of people all interested in developing a generic set
of tools we could all use. Maybe its worth getting all the names together and
setting up a meeting or email list?

Regards,
Kwasi

--
Dr. Kwasi A. Kwakwa
Research Associate, Photonics Group
Physics Department
Imperial College London

On Tuesday 09 Sep 2014 09:05:56 French, Paul  M W wrote:
> Dear all,
>
> What we would like to do at Imperial/Physics with our PALM/STORM data is to
> store the raw data in OMERO and the localisation data associated with it as
> derived from whatever analysis tools we use.  I understand that there is
> not yet a "standard" way to do this - partly because the localisation data
> from the various packages (e.g. QuickPALM, ThunderSTORM etc) are all in
> different formats.

> We also want to be able to visualise the localisation data independently of
> the package used to generate it, in order to be able to do direct
> comparisons.  Ideally we would like a separate (open source) visualisation
> and image analysis tool that can import the localisation data from all the
> various packages.  We could then write our own customised analysis tools to
> work seemlessly with data from the different localisation packages.

> Has this work already been done or do we need to write this ourselves?
>
> Best wishes,
>
> Paul
>
> -----Original Message-----
> From: Jason Swedlow [mailto:j.r.swedlow at dundee.ac.uk<mailto:j.r.swedlow at dundee.ac.uk>]
> Sent: 09 September 2014 05:55
> To: Douglas Russell
> Cc: David Pinto; Joshua Moore; Munro, Ian; Jean-Marie Burel; Ilan Davis;
> Simon Li; French, Paul (PHOT) M W (Photonics)
 Subject: Re:
> Super-resolution data in OMERO
>
> Hi All
>
> Just cc'ing Simon Li on this as his work on the Features API probably aligns
> well with this.

> Cheers,
>
> Jason
>
> Centre for Gene Regulation & Expression | Open Microscopy Environment |
> University of Dundee

> On 8 Sep 2014 18:20, Douglas Russell <douglas.russell at bioch.ox.ac.uk<mailto:douglas.russell at bioch.ox.ac.uk>>
> wrote:
> >
> >
> > Hi all,
> >
> >
> >
> > We are storing/browsing/annotating/downloading/etc super resolution data
> > in OMERO without any problems.
>
> >
> >
> > What we have yet to accomplish to date is some way of joining up the extra
> > data required for localization, deconvolution etc in some OMERO friendly
> > way. We have had some discussions about this and we have a rough plan for
> > implementing an experimental version of this. Something like:
>
> >
> >
> > 1) Store data in OMERO which is public and also available/browseable by
> > all users through the clients so they can browse OTFs etc. It also should
> > be public as we'd like to maintain all the OTFs in one place and there
> > will be tools/people who want to use them outside of OMERO and if they
> > can programmatically access them from their home in OMERO by users
> > without accounts then that's ideal.
>
> >
> >
> > 2) Make use of OMERO.scripts to do the localization/deconvolution/etc
> > using OMERO.grid to provide the horsepower. This is where we are
> > stumbling a little bit. Ideally it would be possible when running a
> > script to do some processing before and during the presentation of the
> > script parameters. For example, the image selected to run the script on
> > can have its metadata analysed to find the suitable OTFs, which can then
> > be presented to the user as a choice. This isn't possible at present so
> > our plan is to allow the user to specify an image ID for the OTF if they
> > wish to override, and otherwise, the script will make a best guess based
> > on the metadata and the date of acquisition.
>
> >
> >
> > 3) Ideally in the long run we'd like to be able to annotate these
> > processing steps, e.g. imageY is derivative of imageX and imageZ was used
> > as the OTF when ABC script was run.
>
> >
> >
> > I have CC'd in David Pinto at Oxford as this concerns him also.
> >
> >
> >
> > Cheers,
> >
> >
> >
> > Douglas
> >
> >
> >
> >
> > On 8 September 2014 18:04, Jason Swedlow <j.r.swedlow at dundee.ac.uk<mailto:j.r.swedlow at dundee.ac.uk>>
> > wrote:
> >
> >>
> >>
> >> Hi All-
> >>
> >>
> >>
> >> Paul called me last week and asked “is anyone storing SR data in
> >> OMERO?”.
> >>
> >>
> >>
> >> One of the biggest challenges we have is knowing what people are doing
> >> with our software.  Normally, we hear when things go wrong, or people
> >> need help with a specific task.  Much more rare is the full statement of
> >> what people are doing, how, why, etc.
>>
> >>
> >>
> >> So we thought of checking with the Oxford Micron/nano gang first, and
> >> then will write to the lists (might be useful to mention anything going
> >> on on the lists anyway).
>>
> >>
> >>
> >> So, Ian and Douglas— any info or ideas that might help Paul et al out?
> >>
> >>
> >>
> >> Cheers,
> >>
> >>
> >>
> >> Jason
> >>
> >>
> >>
> >> --------------------
> >>
> >>
> >>
> >> Centre for Gene Regulation & Expression | Open Microscopy Environment |
> >> University of Dundee
>>
> >>
> >>
> >>
> >>
> >> Phone:  +44 (0) 1382 385819<tel:%2B44%20%280%29%201382%20385819>
> >>
> >>
> >>
> >> email: j.swedlow at dundee.ac.uk<mailto:j.swedlow at dundee.ac.uk>
> >>
> >>
> >>
> >>
> >>
> >> Web: http://www.lifesci.dundee.ac.uk/people/jason-swedlow
> >>
> >>
> >>
> >> Open Microscopy Environment: http://openmicroscopy.org<http://openmicroscopy.org/>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> The University of Dundee is a registered Scottish Charity, No: SC015096
> >
> >
> >
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096

--
Ricardo Henriques, Ph. D.
Senior Lecturer, Academic Lead for Imaging in Biosciences
http://www.ucl.ac.uk/lmcb/research-group/ricardo-henriques-research-group
Interested in advanced microscopy and super-resolution? Join our meetings:
http://www.ucl.ac.uk/lmcb/iq-club
https://mailman.ic.ac.uk/mailman/listinfo/lsr-group

The University of Dundee is a registered Scottish Charity, No: SC015096

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