Re: [h5md-user] Particle tracking

[Peter Colberg]

Hello Mathieu,

Welcome to the H5MD mailing list :-).

On Sun, Sep 01, 2013 at 12:43:18AM +0200, Mathieu Leocmach wrote:
> I like very much the H5MD initiative and I wonder if I could use this
> format to output and share my experimental data.
> 
> I track particles, usually colloids via confocal microscopy. Contrary to
> simulations, I observe only a small portion of the system and particles
> always come in and out of the field of view. Therefore the number of
> particles in a frame is not constant in time and the number of particles
> seen at least once is increasing with time.
> 
> Do you think your file structure can accommodate this type of data?

I think the H5MD file format would be well suited for this data. As
Olaf mentioned, however, the specification currently specifies data
groups for fixed particle number only.

A while ago I proposed [1] an extension to extend the step/time/value
scheme with a range dataset to accommodate variable particle numbers.
Now would be the right time to finalize this proposal.

[1] http://thread.gmane.org/gmane.science.simulation.h5md.user/76

Regards,
Peter