[ome-users] bio-formats MATLAB scripts

[Melissa Linkert]

Hi Pramukta,

The "Alternative scripts" section of http://loci.wisc.edu/bio-formats/matlab
now links to your GitHub repository.

> Sure, that sounds good.  I will also get the loci-tools.jar linked
> to instead of included in the repository in the next week or so.

Thank you!

Regards,
-Melissa

On Mon, Jul 30, 2012 at 02:59:26PM -0400, Pramukta Kumar wrote:
> Sure, that sounds good.  I will also get the loci-tools.jar linked
> to instead of included in the repository in the next week or so.
> -pramukta
> 
> On 07/30/2012 01:21 PM, Melissa Linkert wrote:
> >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
> >>_______________________________________________
> >>ome-users mailing list
> >>ome-users at lists.openmicroscopy.org.uk
> >>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>