[ome-users] bio-formats MATLAB scripts

[Melissa Linkert]

Hi Pramukta,

> I probably should have shared this earlier.  A couple of years back I wrote up some routines that use the bio-formats library to read microscopy datasets directly into MATLAB in a granular fashion.  We tend to generate extremely large datasets in our lab which made using the posted scripts inconvenient (at least at the time, not sure about now) since they would attempt to read in the entire file.  Anyway, the whole thing has been on github for some time now: https://github.com/prakatmac/bf-tools/wiki/about
> 
> Though it does have some limitations, (for example, it doesn't expose all of the metadata), it has worked well for a few other people here for the past couple of years and at least I think it is a pretty convenient interface.  I am going to maintain/update/enhance it for my own work, at least, so hopefully it can be useful to others as well.

Thank you very much for mentioning this.

In the past few months, we have made many enhancements to the MATLAB
scripts posted here:

http://loci.wisc.edu/bio-formats/matlab

that address many if not all of the concerns that you outline.

What I would propose is that we add an extra section at the bottom of
the above page, with a link to your GitHub repository.  That way, anyone
else wishing to use Bio-Formats within MATLAB has a visible choice (or
at least, multiple examples upon which to base their own work).  Does
that sound acceptable?

Please note that it would be best if loci_tools.jar were not
included in the repository, due to licensing differences.  If you can
instead just document which version of loci_tools.jar must be installed
by the user, that would be much appreciated.

Regards,
-Melissa


On Fri, Jul 27, 2012 at 08:44:38AM -0400, Pramukta Kumar wrote:
> I probably should have shared this earlier.  A couple of years back I wrote up some routines that use the bio-formats library to read microscopy datasets directly into MATLAB in a granular fashion.  We tend to generate extremely large datasets in our lab which made using the posted scripts inconvenient (at least at the time, not sure about now) since they would attempt to read in the entire file.  Anyway, the whole thing has been on github for some time now: https://github.com/prakatmac/bf-tools/wiki/about
> 
> Though it does have some limitations, (for example, it doesn't expose all of the metadata), it has worked well for a few other people here for the past couple of years and at least I think it is a pretty convenient interface.  I am going to maintain/update/enhance it for my own work, at least, so hopefully it can be useful to others as well.
> 
> -pramukta
> 
> 
> Pramukta Kumar
> Dynamics Imaging Lab
> Dept of Physics
> Georgetown University

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