Transcript PolySNAP 3 intro - University of Glasgow

Introducing PolySNAP 3
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Introducing
PolySNAP 3
 PolySNAP 3 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 3 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 3 allows up to four different datasets to be analysed
simultaneously
• (or a single dataset with up to four different processing options)
 PolySNAP 3 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
XRD results
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Full profile matching
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XRPD
Patterns
all patterns against all patterns
Correlation
Matrix
Distance
Matrix
Combined
results
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Combine
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Full profile matching
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Raman
Patterns
all patterns against all patterns
Correlation
Matrix
Distance
Matrix
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Distance
Matrix
Raman
results
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Run on…
a single dataset
 Just like PolySNAP:
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- but can now select different kinds of input
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- 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)
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- can also specify a location to load sample image
files from (JPEG files)
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Analysis Tools:
Dendrogram
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Similar patterns are clustered together
Position of ‘Cut-Level’ partitions the data into separate clusters
Too high?
Too low?
Just right
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Adjust the cut-level to best
describe the data
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Analysis Tools:
3D MMDS Plot
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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:
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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 highthroughput 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
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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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Analysis Tools:
Pattern Thumbnail Viewer
 Thumbnail colouring updated as dendrogram cut level is changed
 Helps show which samples are grouped together in which clusters
 Useful visual overview of smaller datasets
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Analysis Tools:
Colour-coded Numeric Results
 Draws the eye to help see patterns in the data
 User-controlled colour scheme and cut-off points
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Analysis Tools:
Peak Overlap Viewer
 Overview of peak intensities and positions throughout the entire
dataset
 Colouring can be user controlled
 See at a glance if peaks coincide or overlap at similar angles
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Run on…
Multiple Datasets
 3 potential ways of working with PolySNAP…
 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
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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
choose data
location
Select
Raman and
choose data
location
Select any
different
processing
options for
each
dataset
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Click OK to
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How much data?
 For each individual dataset, PolySNAP 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:
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PXRD
Raman
DSC
IR
Other spectra data
Numeric
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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
screen to see
information about it
and its profile
displayed below
Click the vertical tabs
to switch between
seeing the PXRD or
Raman profile for the
currently selected
patterns
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Results Screen
 Compare the clustering results from each datatype in turn
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Results Screen
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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-byside
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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
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Form 3
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Form 2
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Form 3
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
Form 2
Forms 3 & 4
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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
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Form 3
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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
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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
• Such 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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Pre-screening
 Have a large dataset of
existing patterns (~100,000) ?
 Compare a single new
unknown sample to the large
dataset in minutes
 Get back a list of top 50 best
matches to the unknown
 Perform PolySNAP clustering &
visualisation on the best
matches
 Pre-screen a large dataset
down to a smaller, more
relevant subset
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Other Features
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Automatic Report Writer
Ability to run from command line - perform 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
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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, prescreening and manual
analysis mode
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Which PolySNAP
Do I Need?
Program Type
Input Data Types
Max No. Of Samples per run
6D plots of sample prep info
Sample JPEG display
Cluster Validation Tools
Report Writer
Re-run selected analysis
No. of clustering methods
Online documentation
Program Tutorial
Customisable Analysis Methods
Manual Matching Options
Interactive Dendrograms
3D MMDS Plots
3D PCA Plots
Numerical Results
Audit-trail Logfile
Amorphous Identification
Reference patterns for mixtures
Command-line run options
Quality Control mode
Combine multiple datasets
Multiple Monitor Support
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PolySNAP M
Commercial
Powder XRD
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No
No
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Yes
Yes
No
Yes
Yes
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PolySNAP 3
Commercial
PXRD, Raman, DSC, IR, Numeric, Other
4x 1500
Yes
Yes
Yes
Yes
Yes
5
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Support Services
 Training
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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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