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

[Seamus Holden]

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


On Mon, 24 Aug 2015 at 10:09 Munro, Ian <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>
> 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
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
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