[ome-devel] Spectral Chemical Imaging Data

[Petr Walczysko (Staff)]

Hi Alan

Thank you for this.
Yes, you are right, the simpler format would be easier. On the other hand, Ian Munro is already doing these first simple tests.

If you would not mind, could you submit the (imzML,  format examples ? It would help us definitely for sorting out
further problems down the line, as this is a topic we want to get better in…

Thank you
All the best
Petr

> On 6 Nov 2015, at 17:09, Alan Race <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<mailto:i.munro at 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<mailto:alan.race at 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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