[ome-devel] Spectral Chemical Imaging Data

[Alan Race]

Hi Ian,
I have logged in and can select the “Experimental Formats” group, but I still don’t see any data. I could be looking in the wrong place I guess?

[cid:image001.png at 01D14942.A78908E0]


Hopefully it shouldn’t be too difficult a task for me to implement a Bio-Formats reader as I’ve already written a library to read imzML data, so theoretically should be able to just call the appropriate methods in that. How would be the best way to go about writing a Bio-Formats reader? Can anyone contribute to the Bio-Formats project?

Thank you very much for the details and the illustration of the data in FLIMfit. The image looks correct, but the spectral dimension looks wrong – is that due to FLIMfit somehow, or should that be displaying the full raw spectral dimension? From your experience, how difficult was it to adapt your tools to be OMERO clients?

Thanks again for all your time and effort,

Alan


From: ome-devel [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of Munro, Ian
Sent: 07 January 2016 09:56
To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk>
Subject: [ome-devel] Spectral Chemical Imaging Data

Happy New Year to you as well Alan.

If you log in again now and change group to “Experimental Formats” you should hopefully be able to see some data under “Mass spec proof of concept/MouseCerebellum”.

If this file format were to be supported in  OME the first step would be to write a Bio-Formats reader.
In order to give a flavour of what that might look like I have attempted to extract the data (N.B. not metadata) from your file and write it into OME-TIFF  files  for which a reader already exists.

The first  file there  “MouseCerebellumC" - I have  mapped your data into the 5D  OME data model with  m/z as channels , which seemed to me most appropriate.
Unfortunately this image is not easy to view using the  standard OMERO clients which, for historical reasons, interpret large numbers of channels as time.

From our earlier discussions, however it seemed likely that you would want a spectrum oriented view so in the second file “MouseCerebellumT” I’ve stored the data as if it were FLIM data with m/z mapped to time(t).
This will allow you examine the data using the FLIMfit tool  http://downloads.openmicroscopy.org/flimfit/4.9.1/
Frustratingly, you  cannot, I’m afraid, log on to the demo server directly from FLIMfit as a version compatible with OMERO 5.2 has not yet been released so it will be necessary to download the file as described in http://help.openmicroscopy.org/export.html#download and open locally.
N.B. you will need to change the background from the default value of 200  to 0.
The screenshot illustrates what I see when I do this.

Obviously I’m not suggesting that FLIMfit is appropriate for your data, but attempting to illustrate  how it might look if you were to adapt your existing tools to be OMERO clients.

I hope all that makes sense.

Best Regards

Ian

[cid:image002.png at 01D14943.C6B237E0]


--
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20160107/2471dc15/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.png
Type: image/png
Size: 96347 bytes
Desc: image001.png
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20160107/2471dc15/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image002.png
Type: image/png
Size: 190800 bytes
Desc: image002.png
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20160107/2471dc15/attachment-0001.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: npl-logo.jpg
Type: image/jpeg
Size: 4543 bytes
Desc: npl-logo.jpg
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20160107/2471dc15/attachment.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: twitter.jpg
Type: image/jpeg
Size: 934 bytes
Desc: twitter.jpg
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20160107/2471dc15/attachment-0001.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: facebook.jpg
Type: image/jpeg
Size: 696 bytes
Desc: facebook.jpg
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20160107/2471dc15/attachment-0002.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: youtube.jpg
Type: image/jpeg
Size: 841 bytes
Desc: youtube.jpg
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20160107/2471dc15/attachment-0003.jpg>