[ome-devel] Spectral Chemical Imaging Data

Wed Nov 18 13:42:34 GMT 2015

Hi Ian,
Yes this is correct. Each spectrum is stored with two arrays, one containing the m/z values and one containing the corresponding intensities, which will both be the same size, but there is no guarantee that every spectrum will have the same length (when the data is stored in “continuous” mode as this data is). The length of each spectrum is stored in the imzML portion of the file as detailed below.

The binaryDataArrayList tag (mzML > run > spectrumList > spectrum > binaryDataArrayList) should contain two binaryDataArray tags, one of which is the details of the m/z array and the other which has the details of the intensity array. The CVParam tags give details of the offset (in bytes in the ibd file) and the encoded length (number of bytes) and the array length (number of elements in the array). The data I have supplied should all be double precision values, but this will be specified in the corresponding referenceableParamGroup tag (mzML > referenceableParamGroupList).

If you would like the Java code that I have written for parsing this for reference (or for testing) I can share that with you.

Regards,
Alan

From: Munro, Ian [mailto:i.munro at imperial.ac.uk]
Sent: 18 November 2015 13:30
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

Hi Again Alan

I’ve started looking at the data you provided.
It  looks as if the spectrum contains a different number of points at each pixel.
Can I ask if that’s correct or have I got the wrong idea.

Best Wishes

Ian

On 6 Nov 2015, at 17:44, Munro, Ian <i.munro at imperial.ac.uk<mailto:i.munro at imperial.ac.uk>> wrote:

Hi Alan

I’v put the screenshot of FLIMfit on our OMER server for you at
https://cisbic.bioinformatics.ic.ac.uk/omero/webclient/?show=image-121463

and there’s more info at http://www.openmicroscopy.org/site/products/partner/flimfit

Since replying I’ve realised that the out-of-the-box clients provided with OMERO may work better for visualising your data than I’d suggested.
They provide the ability to toggle channels on/off at will and display an integrated image of this left ‘on’.

Kind regards

Ian

On 6 Nov 2015, at 17:09, Alan Race <alan.race at npl.co.uk<mailto:alan.race at npl.co.uk>> wrote:

Hello Petr, Ian,
Thank you both for your replies. For some reason I didn't get emailed the replies, I only noticed by browsing the ome-devel archives that you had responded.

The example data is interesting and it certainly does look like there are some parallels between them. We also have the issue that at any particular channel (mass to charge, m/z) we may only detect a few ions and so typically we integrate 10s to 100s of sequential channels (determined by a peak finding algorithm performed on the m/z dimension). I would be very interested in seeing FLIMfit (would it be possible for you to send the screenshot again?).

Petr, I can supply data of pretty much any size for testing purposes (I have single datasets ranging from 10s MB to exceeding 100s GB). There, unfortunately, is no single format that is used by each of the chemical imaging techniques that I am interested in. The most complex format (imzML, http://www.imzml.org/index.php?option=com_content&view=article&id=188&Itemid=63 ) consists of a significant amount of meta data and also caters for (commonly required) sparse storage. I have code written in Java for parsing this, and can certainly share it, but I suspect that for initial testing of clients a simpler format may be better? What do you think?

Kind regards,

Alan

-----Original Message-----
Hello Alan

Further to Ian's answer - would you please be able/willing to give us samples of your data for testing purposes ?
They will be used just for that and not passed on third parties.
The data would enable us to investigate further Ian's suggestion on our (OME) side and find out how our clients cope
with multi-channel data with seriously many channels (among other issues which might appear on the way.).

To submit the files, please go to
https://www.openmicroscopy.org/qa2/qa/upload/
In case they are too big, please let us know and we will provide another solution on how to get the data over to us.

Thank you very much
All the best
Petr

OME Team
Dundee

On 3 Nov 2015, at 20:03, Munro, Ian <i.munro at imperial.ac.uk<http://imperial.ac.uk><mailto:i.munro at imperial.ac.uk<http://imperial.ac.uk>>> wrote:

Hello Alan

From what you say, it sounds as if there may be some parallels between your data and the Fluorescence Lifetime Imaging (FLIM) data that I've been working with.
In the same way the basic unit of FLIM data is a datacube , in this case x,y and time  as opposed to x,y and, I assume, wavelength for your data.

Both OMERO and the OME-tiff standard are designed for up to 5D data:  the 5 dimensions being  x,y,z, Channels and Time.
So I'm confident that your data can easily stored in an OMERO server using the C(hannels) dimension giving you all the advantages
of that.

A sample of our data can be viewed at https://cisbic.bioinformatics.ic.ac.uk/omero/webclient/?show=image-110694
By double-clicking and using the slider you can move through the time dimension and data with many Channels would display in pretty much the same way
with the provided clients.

There are two issues with viewing the data that are unique to FLIM
1)  the raw images  typically contain only a few photons at each time point
2) we are  interested in the rate of decay across time rather than the intensity.

We have therefore developed an OMERO client called FLIMfit that allows this data to be viewed in a more convenient manner and also processed.
Opening the same image with FLIMfit shows a total intensity image on the left and the data at all time points for the chosen pixel on the right (see screenshot).

From your comments my suspicion is that a  similar approach would work well for your data.
Please feel free to contact me if you need further information or indeed a demo given how close we are.

Kind Regards

Dr Ian Munro
Photonics Group
Imperial College, London.

<Screen Shot 2015-11-03 at 19.54.21.png>

Kind Regards

Dr Ian Munro
Photonics Group
Imperial College, London.

On 3 Nov 2015, at 14:19, Alan Race <alan.race at npl.co.uk<http://npl.co.uk><mailto:alan.race at npl.co.uk<http://npl.co.uk>>> wrote:

Hello,
I am currently involved in project that is evaluating various tools for providing a single platform for visualising and processing multi-modality data and was wondering how easy it would be to integrate new types of data into OME. Specifically I am primarily interested in spectral imaging techniques (e.g. mass spectrometry imaging, Raman) where every "pixel" has an associated spectrum and chemical images are generated by integrating over a peak in the spectrum and plotting the resulting sum at the pixel location.

The data can be thought of as a "datacube" or image stack, typically consisting of thousands of images. What underlying structures do you use to handle images? Are there already capabilities to cope with such data?

Thank you for your help,

Alan

Alan Race
Research Scientist
National Physical Laboratory
Hampton Road  |  Teddington  |  TW11 0LW  |  UK
T: +44 (0) 20 8943 6649

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Alan Race
Research Scientist
National Physical Laboratory
Hampton Road  |  Teddington  |  TW11 0LW  |  UK
T: +44 (0) 20 8943 6649

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