[ome-devel] Spectral Chemical Imaging Data

[Josh Moore]

Hi Alan,

On Wed, Nov 18, 2015 at 3:41 PM, Alan Race <alan.race at npl.co.uk> wrote:

> MSiReader uses the code that I wrote to parse imzML (there’s a JAR file
> included in there called imzMLConverter) so it should work well with our
> data.
>
>
>
> The resolution in m/z doesn’t vary from pixel to pixel (potentially very
> slightly, but mass resolution is primarily influenced by the instrument)
> however, only the non-zero intensities are stored and we may detect very
> different ions in any two pixels (hence very different spectra lengths).
> Thank you for your help and insight so far and also for your continued
> efforts.
>

Just a pre-holiday email to let you know that this hasn't dropped off our
radar. Ian was working on extracting the data from your sample file and
storing it first into an OME-TIFF with m/z as channels. This exposed some
limitations in the existing clients when handling data with such a large
number of channels. And second with m/z along the time dimension and a FLIM
style annotation to show what mass spec data might look like if a FLIMfit
style client were written.

A possible next step would be to make these available on a demo server to
discuss possible next steps. Just with the release of OMERO 5.2.1 and the
holidays, that won't be before January.

Hopefully you and yours enjoy the time (one way or the other) until then!

~Josh.




> Regards,
>
> Alan
>
>
>
> *From:* Munro, Ian [mailto:i.munro at imperial.ac.uk]
> *Sent:* 18 November 2015 14:33
> *To:* Alan Race <alan.race at npl.co.uk>
> *Cc:* p.walczysko at dundee.ac.uk; ome-devel at lists.openmicroscopy.org.uk
> *Subject:* Re: [ome-devel] Spectral Chemical Imaging Data
>
>
>
> Thanks Alan
>
>
>
> I’ve started experimenting using this software
> http://www4.ncsu.edu/~dcmuddim/msireader.html  and what I’m seeing
>
> seems to correspond well with your description so I think I’m ok with
> software for now.
>
>
>
> I take it  then that the resolution in m/z varies as well from pixel to
> pixel? If so I may have underestimated the difficulty of storing your data
> into OMERO.  I’ll take this back to the core team for their thoughts.
>
>
>
> Regards
>
>
>
> Ian
>
>
>
>
>
>
>
>
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