dumas ir statistical analysisftp.esrf.eu/.../dumas_ir_statistical_analysis.pdfworkshop «hdf5 as...
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Paul DUMASSOLEIL Synchrotron, France
Multivariate Analysis in Infrared Spectroscopy
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Synchrotron IR data and «« basic »analysis
1000 1500 2000 2500 3000 3500 Wavenumbers (cm-1)
Point spectroscopy
Su
gar
regio
n
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Synchrotron IR data and «« basic »analysis
ChemicalChemical
imagingimaging
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Microscopes are commercial and softwares are proprietary
OPUS ( Bruker)OMNIC( Thermo Fischer)
Essentially used at SR-IR beamlines =
- Facing difficulties for providing the softwares to users
�Since data analysis is time consuming, usersrequest the software for post analysis whenback to their lab or institutes.
- Facing difficulties for exchanging format
�Users request beamtimes at differentbeamlines, and ask for merging data on equivalent samples, from different softwares
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Some developers have madepossible IR data analysis
PyMCA ( A. Solé)
Constraint in file name format, not as friendly-user as the proprietary ones
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Some developers have madepossible IR data analysis
Axis2000 ( A. Hitchcock, C. Jacobsen)
Not as friendly-user as the proprietary ones
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Statistical analysis on spectraand images
data
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Nic
1000 1500 2000 2500 3000 3500
cm-1
Hundreds, even thousands of spectraSubtle difference expected
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Statistical analysis on spectraand images
PCA
HCA LDA Fuzzy-C means
ANN….. K-meansclustering
data
Specific preprocessing required
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Typical example
1000 1500 2000 2500 3000 3500
Wavenumbers (cm-1)
MIE scattering+
Dispersive effect
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
However, single cell spectraare often affected by physical phenomena
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
P.Bassan, H.J. Byrne, F.Bonnier, J.Lee, P.Dumas and Peter Gardner ( The Analyst, 2009)
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
There are data treatment published( not yet satisfactory) to account for these effects
Estimating and Correcting Mie Scattering in Synchrotron-Based MicroscopicFourier Transform Infrared Spectra by Extended Multiplicative Signal Correction KOHLER A. ; SULE-SUSO J. ; SOCKALINGUM G. D. ; TOBIN M. ; BAHRAMI F. ; YANG Y. ; PUANKA J. ; DUMAS P. ; COTTE M. ; VAN PITTIUS D. G. ; PARKES G. ; MARTENS H.Applied spectroscopy 2008, vol. 62, no3, pp. 259-266
Resonant Mie scattering in infrared spectroscopy of biological materials -understanding the 'dispersion artefact' BASSAN Paul ; BYRNE Hugh J. ; BONNIER Franck ; LEE Joe ; DUMAS Paul ; GARDNER Peter Analyst 2009, vol. 134, no8, pp. 1586-1593 [
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
IR data preprocessing
1- Derivative spectra
3500 3000 2500 2000 1500 1000Wavenumbers ( cm-1)
Raw spectrum
First derivative
Second derivative
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
IR data preprocessing
2- Smoothing
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SG 11 points
SG 9 points
SG 7 points
SG 5 points
SG 3 points
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
IR data preprocessing
3- Normalization
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1700 1650 1600 1550 1500Wavenumbers ( cm-1)
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Statistical softwares mostly usedStatistical softwares mostlyused ( all proprietary and
expensives)
� Unscrambler ( www.camo.com)Individual spectra analysis
�Cytospec ( www.cytospec.com)Image analysis
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Importing data in Unscrambler
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Scores Loadings
Influence Explained variance
PCA Output
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
PCA additional features
Selecting spectrainside clusters
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
PCA additional features
Average spectra ofselected points
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
What’s missing in Unscrambler?
�Extracting all spectra from a 2D recording
�PCA of selected frequency ( energy region) region andof two non-adjacent frequency ( energy) regions
�Projecting the scores into the image of re-assembledspectra
Weak points:
Expensive ( between 15k€ to 35k€)
�Beta version of integrated imaging in June 2010
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Hyperspectral imagingwith Cytospec
( Mathlab based-)
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Importing data in Cytospec
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Univariate imaging
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Pre-processing options
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Multivariate imaging options
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
HCA imaging options
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
HCA : cluster imaging
Two clusters
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
HCA : cluster imaging
Three clusters
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Four clusters
HCA : cluster imaging
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
HCA : cluster imagingAverage spectra of each cluster
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Where are the needs?
Routine all exists, needs to reassemble them
Mathematical treatment package
Experiment type ?
IR STXM Diffraction UV fluorescence Others…
« Specific» Menu
X-Fluo
�Spectra treatment and imaging from non-proprietary software
�Statistical analysis of spectra and images , with a common approach for all micro-spectroscopicanalytical tools
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
Where are the needs?
�Merging several spectral range on a same spectra
�Combining with other approaches on the same sample� resolution� probing depth� image alignment
+ +
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Workshop « HDF5 as hyperspectral data analysis format » ESRF January 11-13, 2010 P. Dumas
In summary
Data acquisition is usually achieved using a proprietary software:
* they are all very good but…* difficulties in providing a copy to users* exchange data format difficult,
Statistical approaches do exist, most of the timeproprietary.But niether one is fully satisfactory.. Mathlab routines, IDL… PyMCA are available…
Users demand for software practice after theirexperiment is high, and there is no easy way to fulfil their request.