Introducing Poly SNAP 3

19/04/23Bruker Confidential1

Introducing PolySNAP 3


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


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


Methodology- PXRD + Raman

Full profile matchingall patterns against all patterns

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XRPD Patterns

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Correlation Matrix

Full profile matchingall patterns against all patterns

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Raman Patterns

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Correlation Matrix

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Distance Matrix

Combine

XRD results

Raman results

Combined results

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Distance Matrix

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Distance Matrix




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)


Analysis Tools:Dendrogram

Similar patterns are clustered together Position of ‘Cut-Level’ partitions the data into separate clusters

Adjust the cut-level to best describe the data

Too low?

Just right

Too high?


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


Multiple Methods:Consistent Colouring

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.

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


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.


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.


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 differentshapes

Vary the shape size with temperature, the colour with time

See what initial variables correlate toresulting materials


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


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


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


Analysis Tools:Colour-coded Numeric Results

Draws the eye to help see patterns in the data User-controlled colour scheme and cut-off points


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


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 + Ramano 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


Run on…Multiple Datasets

Select any different

processing options for

each dataset

Select Raman and choose data

location

Select PXRD and

choose data location

Click OK to start


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:

• 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, …


Results Screen


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


Results Screen

Click on the tabs to see different display screens to help you interpret the results


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


Results Screen

Compare the clustering results from each datatype in turn


Results Screen

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


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


Multiple ScreensMultiple Windows

Customers with multiple monitors can open separate results screens on each one, allowing easy comparison of different results side-by-side


Combined DatasetsExample 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




Raman Data only:• Doesn’t distinguish between Form 3 and Form 4

Forms 3 & 4 Form 2




Combined PXRD + Raman using Automatic Weights:• Does much better than the individual methods alone

Form 4 Form 2Form 3


Combine ResultsExample 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




Raman Data only:• E3 and F7 in same cluster!




PXRD&Raman Data Combined:• F7 highlighted as an outlier due to this inconsistency

»

» Other outliers (yellow) are

mixtures of the 2 forms


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


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.


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


Other Features

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


Dealing withLarge 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


PolySNAP M

Ideal for single, smaller datasets (up to 96 patterns) PolySNAP M has dendrograms, 3D plots, prescreening and manual

analysis mode


Which PolySNAPDo I Need?

PolySNAP M PolySNAP 3 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


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


www.bruker-axs.com

www.chem.gla.ac.uk/snap

Documents

Introducing Poly SNAP 3