Introducing Poly SNAP 3 1 Bruker Confidential 16092020

Introducing Poly. SNAP 3 1 Bruker Confidential 16/09/2020

Introducing Poly. SNAP 3 n Poly. SNAP 3 is the successor product to the groundbreaking Poly. SNAP n Poly. SNAP provided powerful cluster analysis tools and clean, elegant and informative graphic displays to allow for high-throughput analysis of Powder X-Ray Diffraction patterns. n Poly. SNAP 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! n Poly. SNAP 3 allows up to four different datasets to be analysed simultaneously • (or a single dataset with up to four different processing options) n Poly. SNAP 3 combines the results from individual datasets to show the overall picture of what’s going on 2 Bruker Confidential 16/09/2020

Multiple Datasets n Combined XRPD + Raman instruments now available – D 8 Spectrolab n Applying multiple techniques to the samples helps give additional information to work with n How would we actually combine results from two such different techniques ? n Automatically calculate optimal weighting for each entry in each dataset • Much more powerful than manually averaging results 3 Bruker Confidential 16/09/2020

Methodology - PXRD + Raman XRD results n Full profile matching nxn XRPD Patterns all patterns against all patterns Correlation Matrix Distance Matrix Combined results nxn Combine n Full profile matching nxn Raman Patterns all patterns against all patterns Correlation Matrix Distance Matrix 4 Bruker Confidential 16/09/2020 Distance Matrix Raman results

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Run on… a single dataset n Just like Poly. SNAP: » - 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 (1 st or 2 nd) » » » 7 Bruker Confidential - can also specify a location to load sample image files from (JPEG files) 16/09/2020

Analysis Tools: Dendrogram n Similar patterns are clustered together n Position of ‘Cut-Level’ partitions the data into separate clusters Too high? Too low? Just right n Adjust the cut-level to best describe the data 8 Bruker Confidential 16/09/2020

Analysis Tools: 3 D MMDS Plot n n n 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 n As with all Poly. SNAP graphics, you can: • • • 9 Zoom in, zoom out, rotate Hide and show and drag labels Change rendering quality Change colour of background, axes etc. Produce figures for publication Bruker Confidential 16/09/2020

Multiple Methods: Consistent Colouring n Changing the clustering in the dendrogram automatically updates the colours in the other plots. n 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. 10 Bruker Confidential 16/09/2020

Analysis Tools: Quantitative Analysis n Given reference phases, Poly. SNAP can identify possible mixtures and perform fast quantitative analysis. Results are shown on the Cell Display in the form of Pie Charts or Stacks. 11 Bruker Confidential 16/09/2020

Analysis Tools: Cell Display n 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. 12 Bruker Confidential 16/09/2020

Analysis Tools: 6 D Plots –Sample Preparation Information n Automatically read sample preparation information from data file headers or standalone CSV file n Plot any combination of this information as different variables in the 3 D plot – vary size, shape and colour of plotted points n e. g. show different solvents as different shapes n Vary the shape size with temperature, the colour with time n See what initial variables correlate to resulting materials 13 Bruker Confidential 16/09/2020

Analysis Tools: Validation n 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 n 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 14 Bruker Confidential 16/09/2020

Analysis Tools: High Dimensionality Viewers n Advanced visualisers to test if the clustering holds true in higher dimensional space n Animated dataset ‘Grand Tour’ n Parallel Coordinates Plots n Space Explorer View 15 Bruker Confidential 16/09/2020

Analysis Tools: Pattern Thumbnail Viewer n Thumbnail colouring updated as dendrogram cut level is changed n Helps show which samples are grouped together in which clusters n Useful visual overview of smaller datasets 16 Bruker Confidential 16/09/2020

Analysis Tools: Colour-coded Numeric Results n Draws the eye to help see patterns in the data n User-controlled colour scheme and cut-off points 17 Bruker Confidential 16/09/2020

Analysis Tools: Peak Overlap Viewer n Overview of peak intensities and positions throughout the entire dataset n Colouring can be user controlled n See at a glance if peaks coincide or overlap at similar angles 18 Bruker Confidential 16/09/2020

Run on… Multiple Datasets n 3 potential ways of working with Poly. SNAP… n 1. Multiple types of data have been collected on the 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? n 2. Multiple instances of the same type of data collected • e. g. PXRD patterns collected on the samples at different times, or under different conditions n 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 19 Bruker Confidential 16/09/2020

Run on… Multiple Datasets Select PXRD and choose data location Select Raman and choose data location Select any different processing options for each dataset 20 Click OK to start Bruker Confidential 16/09/2020

How much data? n For each individual dataset, Poly. SNAP can analyse up to 1, 500 samples at once n Up to four different datasets can be input for each run n 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 n Data formats: RAW, Powder-CIF, ASCII, CSV, Raman SPC, Opus, … 21 Bruker Confidential 16/09/2020

Results Screen 22 Bruker Confidential 16/09/2020

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 23 Bruker Confidential 16/09/2020

Results Screen Click on the tabs to see different display screens to help you interpret the results 24 Bruker Confidential 16/09/2020

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 25 Bruker Confidential 16/09/2020

Results Screen n Compare the clustering results from each datatype in turn 26 Bruker Confidential 16/09/2020

Results Screen » 27 Bruker Confidential Look at both the PXRD and Raman spectra to make sure this clustering looks sensible 16/09/2020

Results Screen Or select up to four multiple datasets to view results side by side… 28 Bruker Confidential 16/09/2020

Multiple Screens Multiple Windows n Customers with multiple monitors can open separate results screens on each one, allowing easy comparison of different results side-byside 29 Bruker Confidential 16/09/2020

Combined Datasets Example 1 n 48 patterns of 3 forms of Sulfathiazol (forms 2, 3 and 4) n PXRD and Raman data collected n PXRD Data only: • Splits form 3 into 2 separate clusters Form 4 30 Form 3 Bruker Confidential Form 2 16/09/2020 Form 3

Combined Datasets Example 1 n 48 patterns of 3 forms of Sulfathiazol (forms 2, 3 and 4) n PXRD and Raman data collected n Raman Data only: • Doesn’t distinguish between Form 3 and Form 4 Form 2 Forms 3 & 4 31 Bruker Confidential 16/09/2020

Combined Datasets Example 1 n 48 patterns of 3 forms of Sulfathiazol (forms 2, 3 and 4) n PXRD and Raman data collected n Combined PXRD + Raman using Automatic Weights: • Does much better than the individual methods alone Form 4 32 Bruker Confidential Form 3 Form 2 16/09/2020

Combine Results Example 2 n 46 patterns of 2 anhydrous forms of Carbamazepeine (Forms 1 & 3) n PXRD and Raman data collected n PXRD Data only: • E 3 and F 7 in different clusters 33 Bruker Confidential 16/09/2020

Combine Results Example 2 n 46 patterns of 2 anhydrous forms of Carbamazepeine (Forms 1 & 3) n PXRD and Raman data collected n Raman Data only: • E 3 and F 7 in same cluster! 34 Bruker Confidential 16/09/2020

Combine Results Example 2 n 46 patterns of 2 anhydrous forms of Carbamazepeine (Forms 1 & 3) n PXRD and Raman data collected n PXRD&Raman Data Combined: • F 7 highlighted as an outlier due to this inconsistency » » 35 Bruker Confidential Other outliers (yellow) are mixtures of the 2 forms 16/09/2020

Combined Results n Matching method does very well in distinguishing forms automatically using either Raman or PXRD data n Combined results using Automatic Weights seem to do better than either PXRD or Raman individually n Identification of pure phases / mixtures improved n 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 n Seeing similar clustering from multiple original data sources increases confidence in the results 36 Bruker Confidential 16/09/2020

Quality Control n 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. ’ n Graphical representation: new samples within the green Pass surface are OK, samples falling outside the surface fail. 37 Bruker Confidential 16/09/2020

Pre-screening n Have a large dataset of existing patterns (~100, 000) ? n Compare a single new unknown sample to the large dataset in minutes n Get back a list of top 50 best matches to the unknown n Perform Poly. SNAP clustering & visualisation on the best matches n Pre-screen a large dataset down to a smaller, more relevant subset 38 Bruker Confidential 16/09/2020

Other Features n n n n n 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 39 Bruker Confidential 16/09/2020

Dealing with Large Datasets n n n n 40 Specially designed tools for dealing with large, complex datasets Select subsets for re-analysis View simplified dendrograms and 3 D plots Show/Hide selected clusters Hide all but current cluster being investigated Transparency options Search options locate individual patterns of interest Bruker Confidential 16/09/2020

Poly. SNAP M n Ideal for single, smaller datasets (up to 96 patterns) n Poly. SNAP M has dendrograms, 3 D plots, prescreening and manual analysis mode 41 Bruker Confidential 16/09/2020

Which Poly. SNAP Do I Need? Program Type Input Data Types Max No. Of Samples per run 6 D 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 3 D MMDS Plots 3 D 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 42 Bruker Confidential Poly. SNAP M Commercial Powder XRD 96 No No No 1 Yes No Yes Yes No No 16/09/2020 Poly. SNAP 3 Commercial PXRD, Raman, DSC, IR, Numeric, Other 4 x 1500 Yes Yes Yes 5 Yes Yes Yes Yes

Support Services n 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 n Customisation • Personalised modifications to suit company-specific workflows • Interface alterations • Integration with other custom-software 43 Bruker Confidential 16/09/2020

www. bruker-axs. com www. chem. gla. ac. uk/snap 44 Bruker Confidential 16/09/2020