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

[Seamus Holden]

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> 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> 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
>
>
> 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
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>>
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