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

Fri Aug 28 11:31:07 BST 2015

I will definitely have a look - but it will take me a week or 2 - grant
applications are getting in the way!

On Fri, 28 Aug 2015 at 11:12 Munro, Ian <i.munro at imperial.ac.uk> wrote:

> 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> 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> 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>_______________________________________________
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>>>>
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