[ome-devel] An attempt to define the problem more clearly(Localization Microscopy)

[Munro, Ian]

Hi Seamus

As I’m currently at an impasse with ThunderSTORM I have added some code to PALM-siever to select and load a file annotation from OMERO
as an example.
Currently this is in my fork at  https://github.com/imunro/palm-siever  but I’m happy to raise a PR if you want to pursue this?

The next step would be to add code to handle Simon’s OMERO table.
For it to work you  also need to download the OMERO matlab plugin code from http://downloads.openmicroscopy.org/omero/5.1.3/.
Just drop the contents into the OMERO.matlab directory that I’ve added.

All the best

Ian



On 26 Aug 2015, at 17:26, Simon Li <spli at dundee.ac.uk<mailto:spli at dundee.ac.uk>> wrote:

Hi Ian, Seamus.

That'd be great. I'm away for two weeks from Friday, but I'm happy to help if you get stuck.

Simon

On 26 August 2015 at 15:21, Munro, Ian <i.munro at imperial.ac.uk<mailto:i.munro at imperial.ac.uk>> wrote:
Hi Seamus

If you want to try this there is quite a bit of code for interfacing matlab applications to OMERO in
https://github.com/openmicroscopy/Imperial-FLIMfit/tree/OME51.

Best Wishes

Ian

On 26 Aug 2015, at 14:58, Seamus Holden <seamus.holden at gmail.com<mailto:seamus.holden at gmail.com>> wrote:

For what it's worth, I'm happy to add this capability to PALMsiever too - not much work.

Best
Seamus

On Tue, 25 Aug 2015 at 14:03 Munro, Ian <i.munro at imperial.ac.uk<mailto:i.munro at imperial.ac.uk>> wrote:
Hi Seamus

Not at all I’m happy to get any feedback  I’m very much feeling my way  here.
In the light of your comments and after discussion with the OME team we have moved on to Plan B. (or possibly E) which is to add to ThunderSTORM
the capability to load  localisations from the data that Simon Li has generated.

Best Wishes

Ian

On 24 Aug 2015, at 11:38, Seamus Holden <seamus.holden at gmail.com<mailto:seamus.holden at gmail.com>> wrote:

Hi Ian

I should stress that although these comments are a bit negative I mean them only in a constructive fashion, and I am completely happy to be contradicted!

There are already a couple of rendering tools available - mainly PALMsiever (which I helped develop, open source), ThunderSTORM (open-source) and VisP (closed source). Being academic software, all of them are a bit buggy, and slowly updated, but essentially, the rendering bit is a (largely) solved problem, software wise. And regards the bugs/ missing features - I would suggest rather than develop new software, just ask for commit rights on PALMsiever or ThunderSTORM - they are both on GitHub!

The common localization format is on the other hand still an unsolved problem.The nicest point to my mind about focussing just on this aspect is that it's a small(-ish), well defined problem, which it would be quite useful to solve.

Best wishes
Seamus
Dr Seamus Holden
University Research Fellow

Centre for Bacterial Cell Biology
Baddiley-Clark Building
Newcastle University
Richardson Road
Newcastle upon Tyne
NE2 4AX, United Kingdom

Phone: +44 (0)191 208 3230<tel:%2B44%20%280%29191%20208%203230>


On Mon, 24 Aug 2015 at 10:09 Munro, Ian <i.munro at imperial.ac.uk<mailto:i.munro at imperial.ac.uk>> wrote:
Hello All

Does anyone have any comments on Kwasi’s document?.
Based on his thoughts  I’ve started looking at developing an open-source OMERO-capable
reconstruction/rendering tool, although not full-time I fear, so progress is slow.

If anyone has any thoughts it would be good to hear them at this early stage.

Thanks

Ian Munro

Photonics Department
Imperial College, London.

On 7 Aug 2015, at 13:43, Kwasi Amoako Kwakwa <k.kwakwa at imperial.ac.uk<mailto:k.kwakwa at imperial.ac.uk>> wrote:

> Hello All,
>
> I am a postdoc in Paul French's group at Imperial working on
> STORM/localization microscopy. I've been talking to Ian Munro a lot trying to
> hash out what I think are the outstanding problems with storing and viewing
> localization data and I thought it might be a good idea to share what I have
> so far and see if people agree and if you have any suggestions or things to
> add.
>
> Thanks,
> Kwasi Kwakwa
>
>
> --
> Kwasi A. Kwakwa
> Research Associate, Photonics Department
> Imperial College London<Localization Microscopy Issues.docx>_______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel

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