EDS Turbocharged!

Keith Thompson
March 2015
 Spectral Imaging, circa 2002

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 Processing of SI data into Maps

There are 3 mechanisms to post-process

maps from an SI data set
X-ray Filters
Net Counts
Phase mapping

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1. x-ray Filters
 How filters work

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 Why filters for x-ray maps?

Extended MHN filter applied to sparse data (< 10 counts per pixel!) and retains
good edges and geometry.

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 Filter application to principal component maps

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2. Net Counts Mapping
X-ray mapping: Raw Counts mapping
Raw counts maps: Integrates the area under a defined ROI.

Mg-K Si-K Fe-K

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 Why Net Counts mapping?

How to interpret spectra like this:

Convolved peaks
Background Raw Counts mapping is routinely WRONG!
Absorption
re-fluorescence Lead?

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 Net Counts: Step 1 Background removal

Background removal with a digital top hat filter

algorithm

Why a top hat filter?

The background varies gradually emulating a
low frequency
Real peaks mimic medium frequency
components
Artifacts mimic high frequency components

The top-hat filter preserves the medium

frequencies (i.e. the real peaks) while
suppressing the high and low frequencies (i.e.
background)

By applying the top-hat filter, the background is

automatically removed.

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 Net Counts

With the background removed the remaining spectrum is well-described by a

combination of pure element reference spectra.

Overlapping peaks are readily de-convolved by iteratively overlaying

the reference spectra until the combination of individual element
spectra matches the background-subtracted spectra.

Fast mode: Few iterations

Fine mode: Many iterations

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Net Counts in mapping . Crisp, clear maps from messy spectra

Raw element maps

Quantitative element maps

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3. Phase Mapping
 Phase Mapping

Energy spectrum per pixel Principal Components Phase Map

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 Why phase mapping?

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 Going Live

Going live = Going Fast

Faster Computers

Fewer variables
Element mapping few identified elements
Fewer pixels dynamic binning

Smarter computing
Normal processing
Using the Intel math libraries
Using all the cores

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 Smarter computing: Math libraries vs. standard compilers

All EDS computation requires intensive

processing algorithms.

Is the person who coded your EDS software

a recognized expert at writing ultra-fast
algorithms that take advantage of the specific
hardware architecture available?

If he says Yes, Hes Probably a liar.

Luckily, the experts at Intel have already coded and optimized many
common scientific computational tasks, and tuned them for their
particular hardware.

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 Math libraries vs. standard compilers

Math functions
Linear algebra: matrix math on core

Intel MKL

Standard compiler

Fast Fourier transforms: broad variety of FFTs in library

Vector math: optimized implementations of computationally intensive core
mathematical operations
Statistics: core/building blocks for statistical analysis

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 Math libraries vs. standard compilers

Intel Math Kernel Libraries and multi-cores

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 Time to complete a Net Counts map - "Fine" mode
9000
6 elemental maps processed
8000
256 512 1024
7000
Processing time (seconds)

6000
5000
4000
3000
2000
1000
0
Standard computingStandard computing Intel Math library Intel Math library
logic logic 64-bit core-threading
32-bit 64-bit 4 cores

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 Time to complete a Net Counts map - "Fine" mode
400
6 elemental maps processed
350
256 512 1024
Processing time (seconds)

300

250

200

150

100

50

0
Standard computingStandard computing Intel Math library Intel Math library
logic logic 64-bit core-threading
32-bit 64-bit 4 cores

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 Time to complete a Net Counts map
250
6 elemental maps processed

200
Processing time (seconds)

1024
Fast mode - 1024
150 256
Fast Mode - 256

100

50
4 seconds < 2 seconds

0
Standard Standard Intel Math library Intel Math library
computing logic computing logic 64-bit core-threading
32-bit 64-bit 4 cores

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 Impact of # of elements

Time to complete a Net Counts map "Fine" mode

1400
Standard computing logic 64-bit
Processing time (seconds)

1200 Intel Math library 64-bit

1000 Intel Math library core-threading 4

cores
800

600

400

200

0
12 9 6 3
# of elements in map

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 Conclusion

Spectral Imaging has enabled post-processing of the EDS

x-ray maps
X-ray filters
Net Counts & Quantitative mapping
Phase mapping

Going Live = Going FAST

Not just a fast computer
Using the computer to its fullest extent

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