[Neurodebian-upstream] [Neurodebian-devel] poster copy request

[Jan Benda]

Hi,

one should really distinguish between real-time and online electrophysiology.
Realtime would be anyting that uses a real-time kernel like RTAI and allows to 
make calculations on a per sample basis (kHz range). The software doing this 
and being out for quite some time is Rtxi http://www.rtxi.org. My RELACS 
www.relacs.net also supports this kind of realtime acquisition and 
computation.

All the other data acquisition software seems to do online analysis, i.e. 
shows you some data and processed results on the fly. But this usually is 
done in user space by taking the data every few milliseconds.

From looking what Bluespike does I would say it is an online type program, but 
it still uses RTAi and a kernel module for data acquisition. From how many 
channels can you record? Do you use comedi's comedi_data_read and _write 
functions, or do you use streaming acquisition with callbacks?

Jan



On Friday 28 January 2011 09:51:35 Yury V. Zaytsev wrote:
> Hey!
>
> Just saw you bounced half of your mailbox to the list and felt a sudden
> urge to chime in...
>
> On Fri, 2010-11-19 at 09:33 -0500, Yaroslav Halchenko wrote:
> > Have you seen other interesting Linux-based RT electrophysiology
> > acquisition/analysis projects at SfN10?
>
> Disclaimer: I've NOT been to SfN.
>
> It depends on what do you mean by realtime. I think a rough
> classification would include "soft" realtime which can be achieved with
> non-RT kernels and "hard" realtime which you can only achieve by using
> the RT patchset and what follows.
>
> >From what I know, there is a number of realtime EP acquisition systems
>
> available under FOSS licences which have been around for quite some
> time. Of course, there are also some commercial systems developed for a
> very particular task or having some special hardware in mind.
>
> There have recently been a small meeting of the developers of such
> systems at my institution:
>
> http://neuralensemble.org/trac/cole/wiki/COLE_2010
>
> There is not so much to see there, but you can download the list of
> participants and get an idea on who is involved.
>
> I can mention at least three systems without doing any prior research:
>
> 1) NeurOnline (developed at my institution)
> 2) RELACS [1] appears to be the oldest out there
> 3) MEABench [2] more geared towards MEAs
>
> The main goal of the meeting was to mitigate the NIH syndrome and
> concentrate on developing common standardized components instead of keep
> on re-inventing wheels of different calibers.
>
> [1]: http://relacs.sourceforge.net/
> [2]: http://www.its.caltech.edu/~daw/meabench/
>
> > It was our impression from SfN10, that there exist various very
> > interesting but disjoint efforts which might  benefit greatly if forces
> > get joined or at least centralized to some degree.
>
> This was our impression as well, hence COLE was created.
>
> I will forward the link to this thread to some of the attendants. Maybe
> if they are interested they can join the discussion or otherwise just
> have a look at it.
>
> > On our hand we could help making Debian (and thus its derivatives such
> >  as ubuntu) convenient out-of-the-box for such kind of research.
>
> Well... I am not sure that apart from RELACS there is other software
> that is so to say deployment-ready. From my experience, compilation and
> installation is actually the least complicated part of getting the setup
> running, what is really challenging is the configuration process.
>
> Often, the hardware is working somehow differently depending on the
> platform and you often need to re-compile after you figure out what the
> differences are etc.
>
> So in this sense I am not sure if the packages as such are going to be
> of huge help, since it's generally easier for users to install to /opt
> instead of learning how to rebuild the packages.
>
> What would really need packaging in my opinion are libraries. Having all
> dependencies and pre-requisites packaged would definitively help a lot.
>
> HTH,



-- 
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Dr. Jan Benda
Biozentrum der LMU                             phone: +49 / 89 - 2180 74805
Department Biologie II                           FAX: +49 / 89 - 2180 74803
Grosshaderner Str. 2                            room: D01 043
D - 82152 Planegg-Martinsried
Germany                                 web: <http://www.bio.lmu.de/~benda>

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