[SciPy-User] [ANN] release of Neo 0.2.0

Samuel Garcia sgarcia@olfac.univ-lyon1...
Thu Feb 16 11:57:56 CST 2012


Of course.
A global convergence would great! (neo team already plane to propose to 
merge with nitime).

But at the moment it is not so easy:
  nitime = object model + analysis
  nibabel = IO collections for NI
  neo = object model + IO collection for electrophysiology

The main work is that nitime's object model and neo's object model differ.
nitime objects are neutral.
Neo object are colored for the use.For example, neo also add containers 
objects ("one to many" and "many to many" relationship between object)

But doing a conversion script could be very easy (if loosing the 
relationship between objects):
neo.AnalogSignal >>> nittime.TimeSerie
neo.SpikeTrain >>> nittime.TimeArrays
neo.EpochArray >>> list of nitime.Epoch
neo.EventArray >>> list of nitime.Event
neo.Epoch >>> nitime.Epoch
neo.Event >>> nitime.Event







Le 15/02/2012 23:00, Ariel Rokem a écrit :
> Hi Samuel,
>
> Congratulations on the release!
>
> Concerning the comparison with nitime: At the moment, support for 
> reading data from files in nitime is only implemented for neuroimaging 
> data (using nibabel as an optional dependency, only for this bit), but 
> the core classes in nitime can be used for any kind of time-series 
> data (including data from single-cell recordings: 
> http://nipy.sourceforge.net/nitime/examples/grasshopper.html), 
> assuming the data has already somehow been read into numpy arrays. In 
> fact, it would be great to have io functions in nitime which read data 
> using neo and initialize nitime.TimeSeries objects for further analysis.
>
> Cheers,
>
> Ariel
>
>
>
> On Wed, Feb 15, 2012 at 12:58 AM, Samuel Garcia 
> <sgarcia@olfac.univ-lyon1.fr <mailto:sgarcia@olfac.univ-lyon1.fr>> wrote:
>
>     Nitime is oriented for time series of neuro imaging.
>
>     Neo offer a complete data model center around electrophysiology
>     (in vivo
>     or simulations) with more objects than nitime (for this fields of
>     course):
>     RecodingChannelGroup +RecodingChannel + Segment + Block +Unit+...
>
>     Samuel
>
>
>
>
>
>     Le 14/02/2012 16:15, Larry Eisenman a écrit :
>     > Samuel Garcia<sgarcia<at> olfac.univ-lyon1.fr
>     <http://olfac.univ-lyon1.fr>>  writes:
>     >
>     >>
>     >>      Dear scipy list,
>     >>      We are proud to announce the 0.2.0 release of Neo, a
>     Python library for
>     > working with
>     >>      electrophysiology data, whether from biological
>     experiments or from
>     >>      simulations.
>     > ....
>     >
>     > How does this compare/relate to the Nitime module of the Nipy
>     project
>     > (http://nipy.sourceforge.net/nitime/)?
>     >
>     > Larry
>     >
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>     --
>     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>     Samuel Garcia
>     Lyon Neuroscience
>     CNRS - UMR5292 -  INSERM U1028 -  Universite Claude Bernard LYON 1
>     Equipe R et D
>     50, avenue Tony Garnier
>     69366 LYON Cedex 07
>     FRANCE
>     Tél : 04 37 28 74 24
>     Fax : 04 37 28 76 01
>     http://olfac.univ-lyon1.fr/unite/equipe-07/
>     http://neuralensemble.org/trac/OpenElectrophy
>     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
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-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Samuel Garcia
Lyon Neuroscience
CNRS - UMR5292 -  INSERM U1028 -  Universite Claude Bernard LYON 1
Equipe R et D
50, avenue Tony Garnier
69366 LYON Cedex 07
FRANCE
Tél : 04 37 28 74 24
Fax : 04 37 28 76 01
http://olfac.univ-lyon1.fr/unite/equipe-07/
http://neuralensemble.org/trac/OpenElectrophy
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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