[ome-devel] Spectral Chemical Imaging Data

[Munro, Ian]

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:4323764B-1BA7-45ED-A470-CD70A12261AC at home]

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20160107/b9ff2b83/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2016-01-07 at 09.53.34.png
Type: image/png
Size: 331406 bytes
Desc: Screen Shot 2016-01-07 at 09.53.34.png
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20160107/b9ff2b83/attachment.png>