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

[Seamus Holden]

Looks great! - I'll test it and push it to the main branch asap

On 17:50, Wed, 9 Sep 2015 Munro, Ian <i.munro at imperial.ac.uk> wrote:

> Hello
>
> I have now added the ability to import data from the table that Simon
> created, to PALM-siever.
> Screenshots attached. Code in https://github.com/imunro/palm-siever
>
>  It’s currently quite slow, however.
>
> Best Wishes
>
> Ian
>
>
>
>
>
> On 26 Aug 2015, at 15:21, Ian Munro <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> 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> 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
>>> 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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