[ome-devel] Spectral Chemical Imaging Data

[Petr Walczysko (Staff)]

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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