[ome-users] [Software Feedback] MATLAB bfopen discards series names

[Curtis Rueden]

Hi Allon,

I am CCing the ome-users list, which is the best place to ask Bio-Formats
questions.

> I just started using your matlab functions with loci-tools.jar. Thanks
> for making a wonderful tool!

Glad to hear it is working for you.

> I noticed a problem, which I suspect has a quick fix. When loading
> multiple series from a .lif file with bfopen, the image "labels" do
> not include the original series title. Instead, the bfopen script
> creates a "meaningful" label that includes information such as "series
> 1/23", but not the actual series label.

Indeed, it happens here:

https://github.com/openmicroscopy/bioformats/blob/v4.4.8/components/bio-formats/matlab/bfopen.m#L200

> This is clearly a matlab-implementation specific issue, because the
> series names are correctly recognized in the imageJ importer.

Right.

> I wonder whether you can suggest a quick hack to add this information?
> I tried looking up a user guide for loci-tools.jar, to see what
> command might retrieve the series names. But I couldn't find any
> information.

Sure, the code would be something like:

# override label with series name, if available
imageName = r.getMetadataStore().getImageName(i);
if imageName ~= ""
  label = imageName;
end

But I have not tested this, so it may need minor tweaking.

Regards,
Curtis


On Thu, Jun 13, 2013 at 9:13 AM, <allon_klein at hms.harvard.edu> wrote:

> Allon Klein sent a message using the contact form at
> http://loci.wisc.edu/contact.
>
> Hi,
>
> I just started using your matlab functions with loci-tools.jar. Thanks for
> making a wonderful tool!
>
> I noticed a problem, which I suspect has a quick fix. When loading
> multiple series from a .lif file with bfopen, the image "labels" do not
> include the original series title. Instead, the bfopen script creates a
> "meaningful" label that includes information such as "series 1/23", but not
> the actual series label.
>
> This is clearly a matlab-implementation specific issue, because the series
> names are correctly recognized in the imageJ importer.
>
> For me having the series names is critical, since each series refers to a
> different condition and the details are stored in the names.
>
> I wonder whether you can suggest a quick hack to add this information? I
> tried looking up a user guide for loci-tools.jar, to see what command might
> retrieve the series names. But I couldn't find any information.
>
> Thanks very much, in advance, for your help!
>
> Best wishes,
> Allon Klein
> Systems Biology
> Harvard Medical School
>
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