[ome-devel] Spectral Chemical Imaging Data

[Jean-Marie Burel (Staff)]

Hi Alan

Thanks, very helpful

Jmarie

From: ome-devel <ome-devel-bounces at lists.openmicroscopy.org.uk<mailto:ome-devel-bounces at lists.openmicroscopy.org.uk>> on behalf of Alan Race <alan.race at npl.co.uk<mailto:alan.race at npl.co.uk>>
Reply-To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
Date: Monday, 18 January 2016 14:35
To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-devel] Spectral Chemical Imaging Data

Hi Jean-Marie,
As discussed, here is a link to some open software that will allow you to look at data in the imzML format (http://www4.ncsu.edu/~dcmuddim/msireader.html). It’s not so easy to view a single spectrum in that software, so I have included an image taken from our internal software that shows what the spectrum (where the x-axis is m/z and the y-axis is intensity) at location (40, 20) looks like along with the TIC image (the sum of all ion images present within the dataset).

[cid:image001.png at 01D151FD.6DD89020]

Thanks,

Alan

From: ome-devel [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of Jean-Marie Burel (Staff)
Sent: 11 January 2016 14:42
To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-devel] Spectral Chemical Imaging Data

Hi Alan

I had a brief chat today with Ian and we thought it will be good to maybe have a discussion later on this week.
Will Thursday at 2pm work you?

Cheers
Jmarie



From: ome-devel <ome-devel-bounces at lists.openmicroscopy.org.uk<mailto:ome-devel-bounces at lists.openmicroscopy.org.uk>> on behalf of Alan Race <alan.race at npl.co.uk<mailto:alan.race at npl.co.uk>>
Reply-To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
Date: Thursday, 7 January 2016 14:20
To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-devel] Spectral Chemical Imaging Data

Hi Ian,
I’ve started trying to read about 8D OME storage (https://www.openmicroscopy.org/site/support/ome-model/developers/6d-7d-and-8d-storage.html ), but I think I need to become a little more familiar with OME to know which option will map best to our data.

I can certainly help shed some light on number 2 though. A lot of the metadata included within the file is to do with how the data should be read in, parsed, processed etc. and can be handled by my library/the bio-formats reader and isn’t necessary for the end user to see.

The remaining metadata helps to describe the experiment (ideally in sufficient detail that it could be repeated) and it would be useful to be able to view/query this, but that isn’t necessarily a priority. All of the metadata can be boiled down to (tag, value) pairs, where there are very few *required* tags, and the majority are optional descriptors organised in a hierarchy (http://www.peptideatlas.org/tmp/mzML1.1.0.html ). Is there an equivalent of the Bio-Formats reader for metadata? How is metadata typically stored for other formats?

Best wishes,

Alan


From: ome-devel [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of Munro, Ian
Sent: 07 January 2016 12:58
To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-devel] Spectral Chemical Imaging Data

Hi Alan

That would certainly be the best way to get things moving.
There  are two questions that need to be addressed first though.

1) How best to fit this data into the 8D OMERO model ? I tried 2 options, as examples,  but there are many other possibilities.

2) What to do about metadata? Which depends I suspect on your needs.

Hopefully the core OMERO  may have some input here.

Best Wishes

Ian


On 7 Jan 2016, at 12:36, Alan Race <alan.race at npl.co.uk<mailto:alan.race at npl.co.uk>> wrote:

Hi Ian,
Okay great, thanks, that worked and I can download the data and open in FLIMfit. This style of viewing/processing with our current tools but with the OMERO backend would actually be great.

I’m not sure if you saw my additional questions below the image in the previous email, but as for the next step, what do you think would be the best way to proceed? I suspect that probably it would be for me to write a Bio-Formats reader for imzML?

Best wishes,

Alan



From: ome-devel [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of Munro, Ian
Sent: 07 January 2016 12:16
To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-devel] Spectral Chemical Imaging Data

Hi Alan

Sorry I should have said that you need to select user Ian Munro when you select the group.
By default the OMERO clients show you your own data only.

Ian <image001.png>


On 7 Jan 2016, at 12:06, Alan Race <alan.race at npl.co.uk<mailto:alan.race at npl.co.uk>> wrote:

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?

<image001.png>


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<mailto: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

<image002.png>

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