[ome-devel] Spectral Chemical Imaging Data

[Alan Race]

Hi Josh,
Thank you for your email and the information on current progress. The number of channels in the data can certainly be a challenge. The data that I shared was actually relatively low mass resolution data (Fourier Transform based instruments can produce spectra with an order of magnitude more channels). No worries about the delay though. If there is any way that I can help in this I would be very happy to, feel free to get in touch.

Happy holidays,

Alan

From: ome-devel [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of Josh Moore
Sent: 17 December 2015 15:56
To: <ome-devel at lists.openmicroscopy.org.uk> <ome-devel at lists.openmicroscopy.org.uk>
Subject: Re: [ome-devel] Spectral Chemical Imaging Data

Hi Alan,

On Wed, Nov 18, 2015 at 3:41 PM, Alan Race <alan.race at npl.co.uk<mailto: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<mailto:i.munro at imperial.ac.uk>]
Sent: 18 November 2015 14:33
To: Alan Race <alan.race at npl.co.uk<mailto:alan.race at npl.co.uk>>
Cc: p.walczysko at dundee.ac.uk<mailto:p.walczysko at dundee.ac.uk>; ome-devel at lists.openmicroscopy.org.uk<mailto: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




________________________________

[cid:image001.jpg at 01D138E6.1CFBE9C0]<http://www.npl.co.uk/?utm_source=Email%20Footer&utm_medium=email&utm_campaign=Homepage>

Keep in touch by signing up for an email newsletter<http://www.npl.co.uk/keep-in-touch/?utm_source=Email%20Footer&utm_medium=email&utm_campaign=Newsletter> [cid:image002.jpg at 01D138E6.1CFBE9C0] <http://www.twitter.com/npl> [cid:image003.jpg at 01D138E6.1CFBE9C0] <http://www.facebook.com/npldigital> [cid:image004.jpg at 01D138E6.1CFBE9C0] <http://www.youtube.com/npldigital>

________________________________
If you have received this message in error, please notify us and remove it from your system.
NPL Management Ltd cannot guarantee that the e-mail or any attachments are free from viruses.

NPL Management Ltd is a company registered in England and Wales, number: 2937881
Registered office: National Physical Laboratory | Hampton Road | Teddington, Middlesex | UK | TW11 0LW


_______________________________________________
ome-devel mailing list
ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20151217/80932129/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.jpg
Type: image/jpeg
Size: 4543 bytes
Desc: image001.jpg
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20151217/80932129/attachment.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image002.jpg
Type: image/jpeg
Size: 934 bytes
Desc: image002.jpg
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20151217/80932129/attachment-0001.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image003.jpg
Type: image/jpeg
Size: 696 bytes
Desc: image003.jpg
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20151217/80932129/attachment-0002.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image004.jpg
Type: image/jpeg
Size: 841 bytes
Desc: image004.jpg
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20151217/80932129/attachment-0003.jpg>