Introducing PolySNAP 2

1 Bruker Confidential 02/11/2007

Introducing
PolySNAP 2

PolySNAP 2 is the successor product to the groundbreaking PolySNAP

PolySNAP provided powerful cluster analysis tools and clean, elegant

and informative graphic displays to allow for high-throughput analysis
of Powder X-Ray Diffraction patterns.

PolySNAP 2 has the same powerful tools, but allows them to be

employed to ANY kind of numeric data
• PXRD, Raman, IR, DSC, Melting Points…. Anything!

PolySNAP 2 allows up to four different datasets to be analysed

simultaneously
• (or a single dataset with up to four different processing options)

PolySNAP 2 combines the results from individual datasets to show the

overall picture of what’s going on

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Multiple Datasets

Combined XRPD + Raman instruments now available – D8 Spectrolab

Applying multiple techniques to the same samples helps give

additional information to work with

How would we actually combine results from two such different

techniques ?

Automatically calculate optimal weighting for each entry in each

dataset
• Much more powerful than manually averaging results

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 Methodology
- PXRD + Raman

n Full profile matching nxn nxn XRD results

all patterns against all patterns Correlation Distance

XRPD
Matrix Matrix Combined
Patterns
results

nxn
Combine Distance
Matrix

n Full profile matching nxn nxn

all patterns against all patterns Correlation Distance
Raman Raman
Matrix Matrix
Patterns results

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Run on…
a single dataset

Just like PolySNAP:

» - but can now select different kinds of input

» - Separate automatic pre-processing defaults for

each type of data
» - also new is the ability to transform spectra
» - either Fourier transform or derivative (1st or 2nd)

» - can also specify a location to load sample image

files from (JPEG files)

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 Analysis Tools:
Dendrogram

Similar patterns are clustered together

Position of ‘Cut-Level’ partitions the data into separate clusters

Too high?

Too low?

Just right

Adjust the cut-level to best

describe the data

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Analysis Tools:
3D MMDS Plot

Each sphere is a pattern

The closer together two spheres are, the more similar they are

Similar patterns ‘clump’ together

Different patterns are far apart

Easy to spot outliers at a glance

As with all PolySNAP graphics, you can:

• Zoom in, zoom out, rotate
• Hide and show and drag labels
• Change rendering quality
• Change colour of background, axes etc.
• Produce figures for publication

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Multiple Methods:
Consistent Colouring

Changing the clustering
in the dendrogram
automatically updates
the colours in the other
plots.

Cluster colours from dendrogram

are used on MMDS plot so you can
compare the groupings from both
methods. Same results from both
increases confidence in the
accuracy of the results.

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Analysis Tools:
Quantitative Analysis

Given reference phases, PolySNAP can identify possible mixtures and

perform fast quantitative analysis. Results are shown on the Cell
Display in the form of Pie Charts or Stacks.

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Analysis Tools:
Cell Display

Cell Display is also

useful for seeing the
clustering result
colours superimposed
on e.g. the layout of
an original 96 well
plate from a high-
throughput system.

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Analysis Tools:
6D Plots –Sample Preparation Information

Automatically read sample preparation information from data file

headers or standalone CSV file

Plot any combination of this information as different variables in the
3D plot – vary size, shape and colour of plotted points

e.g. show different solvents as different
shapes

Vary the shape size with temperature,
the colour with time

See what initial variables correlate to
resulting materials

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Analysis Tools:
Validation

Check the validity of the clustering using powerful statistical tests

• Silhouettes – are these cluster memberships reasonable?
• Fuzzy Clustering – should this pattern be in a different cluster?
• Scree plots – how many clusters are needed to explain the data?
• Minimum Spanning Trees – an alternative way to construct clusters

Silhouettes example:
• Pattern 21 scores poorly as a member of this cluster
• it is the least tightly connected in the dendrogram
• This turns out to be a mixture, rather than a pure phase

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Analysis Tools:
High Dimensionality Viewers

Advanced visualisers to test if the clustering holds true in higher

dimensional space

Animated dataset ‘Grand Tour’

Parallel Coordinates Plots

Space Explorer View

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Run on…
Multiple Datasets

3 potential ways of working with PolySNAP 2…

1. Multiple types of data have been collected on the same samples

• e.g. there is a set of 96 samples, from which have been collected both
PXRD and Raman spectra
• Examine the clustering from the PXRD, and the Raman, and the combined
PXRD + Raman
o Do the different methods agree? Do they contradict each other?

2. Multiple instances of the same type of data collected

• e.g. PXRD patterns collected on the same samples at different times, or
under different conditions

3. Investigate a single dataset under different processing options

• Compare side-by-side what difference turning background subtraction, etc.
on makes to the final results

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 Run on…
Multiple Datasets
Select
PXRD and Select
choose data Raman and
location choose data
location

Select any
different
processing
options for
each
dataset Click OK to
start

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How much data?

For each individual dataset, PolySNAP 2 can analyse up to 1,500

samples at once

Up to four different datasets can be input for each run

The datasets can be any combination of:
• PXRD
• Raman
• DSC
• IR
• Other spectra data
• Numeric
o Numeric can be a correlation matrix, or ‘raw’ numeric data relating to the samples
being analysed
– e.g. Melting points

Data formats: RAW, Powder-CIF, ASCII, CSV, Raman SPC, Opus

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Results Screen

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Results Screen

Click on the dataset

name to switch
between different sets
of results – here,
choose between
PXRD and Raman
individually, or the
combined results

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Results Screen

Click on the tabs to

see different display
screens to help you
interpret the results

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Results Screen

Select a sample or
samples in the results
Click the vertical tabs screen to see
to switch between information about it
seeing the PXRD or and its profile
Raman profile for the displayed below
currently selected
patterns

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Results Screen

Compare the clustering results from each datatype in turn

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Results Screen

» Look at both the PXRD and Raman spectra to make sure this
clustering looks sensible

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Results Screen
Or select up to four
multiple datasets to view
results side by side…

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Multiple Screens
Multiple Windows

Customers with multiple monitors can open separate results screens

on each one, allowing easy comparison of different results side-by-
side

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Combined Datasets
Example 1

48 patterns of 3 forms of Sulfathiazol (forms 2, 3 and 4)

PXRD and Raman data collected

PXRD Data only:

• Splits form 3 into 2 separate clusters

Form 4 Form 3 Form 2 Form 3

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Combined Datasets
Example 1

48 patterns of 3 forms of Sulfathiazol (forms 2, 3 and 4)

PXRD and Raman data collected

Raman Data only:

• Doesn’t distinguish between Form 3 and Form 4

Forms 3 & 4 Form 2

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Combined Datasets
Example 1

48 patterns of 3 forms of Sulfathiazol (forms 2, 3 and 4)

PXRD and Raman data collected

Combined PXRD + Raman using Automatic Weights:

• Does much better than the individual methods alone

Form 4 Form 3 Form 2

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Combine Results
Example 2

46 patterns of 2 anhydrous forms of Carbamazepeine (Forms 1 & 3)

PXRD and Raman data collected

PXRD Data only:

• E3 and F7 in different clusters

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Combine Results
Example 2

46 patterns of 2 anhydrous forms of Carbamazepeine (Forms 1 & 3)

PXRD and Raman data collected

Raman Data only:

• E3 and F7 in same cluster!

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Combine Results
Example 2

46 patterns of 2 anhydrous forms of Carbamazepeine (Forms 1 & 3)

PXRD and Raman data collected

PXRD&Raman Data Combined:

• F7 highlighted as an outlier due to this inconsistency
»

» Other outliers (yellow) are

mixtures of the 2 forms

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Combined Results

Matching method does very well in distinguishing forms automatically

using either Raman or PXRD data

Combined results using Automatic Weights seem to do better than
either PXRD or Raman individually

Identification of pure phases / mixtures improved

Use of combined data highlights any inconsistencies in separate
analyses
• Sunch inconsistencies would not be obvious with only one data source
• User can then examine outliers manually in detail

Seeing similar clustering from multiple original data sources increases
confidence in the results

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Quality Control

Given a set of reference patterns, new patterns can be considered to

be similar enough to the references to ‘pass’, or different enough to
‘fail.’

Graphical representation:
new samples within the green
Pass surface are OK, samples
falling outside the surface fail.

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Other Features

Automatic Report Writer

Ability to run from command line - launch analysis as part of a script

Integration with other Bruker software

Audit-trail detailed logfile

Raw numeric results available for interrogation

Results automatically archived to encrypted file

Full manual and tutorial provided

View sample images alongside patterns

Manual analysis mode:
• Compare one pattern to many
• Detailed numeric breakdown of results

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Dealing with
Large Datasets

Specially designed tools for dealing with large, complex datasets

Select subsets for re-analysis

View simplified dendrograms and 3D plots

Show/Hide selected clusters

Hide all but current cluster being investigated

Transparency options

Search options locate individual patterns of interest

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PolySNAP M

Ideal for single, smaller datasets (up to 96 patterns)

PolySNAP M has dendrograms, 3D plots, and manual analysis mode

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 Which PolySNAP
Do I Need?
PolySNAP M PolySNAP 2
Program Type Commercial Commercial
Input Data Types Powder XRD PXRD, Raman, DSC, IR, Numeric, Other
Max No. Of Samples per run 96 4x 1500
6D plots of sample prep info No Yes
Sample JPEG display No Yes
Cluster Validation Tools No Yes
Report Writer No Yes
Re-run selected analysis No Yes
No. of clustering methods 1 5
Online documentation Yes Yes
Program Tutorial Yes Yes
Customisable Analysis Methods No Yes
Manual Matching Options Yes Yes
Interactive Dendrograms Yes Yes
3D MMDS Plots Yes Yes
3D PCA Plots Yes Yes
Numerical Results Yes Yes
Audit-trail Logfile Yes Yes
Amorphous Identification Yes Yes
Reference patterns for mixtures Yes Yes
Command-line run options No Yes
Quality Control mode No Yes
Combine multiple datasets No Yes
Multiple Monitor Support No Yes

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Support Services

Training
• One and two-day in-depth training packages available
• Gain detailed knowledge of advanced program functions
• Use advanced options with trickier datasets with confidence
• Look at your own data with

Customisation
• personalised modifications to suit company-specific workflows
• Interface alterations
• Integration with other custom-software

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 www.bruker-axs.com
www.chem.gla.ac.uk/snap

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