1. Introduction

1.1. Welcome

Welcome to SMDExplorer. SMDExplorer is an integrated, cross-platform program to analyze and visualize spectroscopic data obtained from the Tokyo Instruments Nanofinder and Phalanx instruments.

Key features of SMDExplorer include:

• native input and output of raw instrument data as well as conversion to industry standard formats

• a wide range of data preprocessing techniques to make the most of your data

• standard analysis (e.g. intensity profiles or ratios) of one-, two-, and three-dimensional data

• automated image formation for automatic, one-click analysis of spectral datasets to extract characteristic chemical entities and their distributions

• peak deconvolution of one-, two-, and three-dimensional data with an unlimited number of peaks to extract spectral parameters

• particle analysis to compute image metrics

• publication-quality graphics output in a wide variety of formats

• sensible presets to make data processing and analysis easy out-of-the-box

• interoperability with third-party software

• light-weight and cross-platform

SMDExplorer was designed for both novice and expert spectroscopists with a focus on making routine analysis easy while still providing full control to power users.

The Guided Tour provides an essential orientation over the features of SMDExplorer and is recommended for all users. The remainder of this manual contains further details and references on the processing and analysis functionality of SMDExplorer.

1.2. What’s New

1.2.1. SMDExplorer 1.0.5 (‘New Rules’)

1.2.1.1. New Features

• preprocessing settings can now be saved and loaded from disk

• batch pre-processing

• GPU-accelerated peak deconvolution

• trace colors can be selected manually

1.2.2. SMDExplorer 1.0.4 (‘Hallucinate’)

1.2.2.1. New features

• spectral stitching for spectra acquired at overlapping wavelength ranges, e.g. via a grating scan

• color maps can now be inverted in the axis dialogue

• performance improvements to 3D display of large datasets

• added two additional smoothing methods (windowed Savitzky-Golay smoothing and Whittaker smoothing)

• the 3D imaging clipping plane can now be rotated

• the point cloud volumetric rendering mode is now more visually pleasing

• individual slices of a 3D dataset can now be saved

• improvements to the Linux version of SMDExplorer

• added JCAMP-DX export

• support for reading .sif files (single spectra or kinetic series)

1.2.3. SMDExplorer 1.0.3 (‘Levitating’)

1.2.3.1. New features

• added the DHO line shape.

• added noise-corrected principal component analysis (NC-PCA).

• two- and three dimensional graphs can now be displayed with a scale bar instead of a set of axes.

• constraints during peak fitting can now be deactivated, resulting in a significant speedup of peak deconvolution for well-behaved datasets.

• added different levels of default constraints as starting points for user customization.

• isosurfaces can now be exported as 3D Wavefront .obj files.

• improvements to waterfall plots:

  • the fill color is now drawn correctly for data with a convex baseline

  • plots now can be exported as animation files

• improved reordering / renaming of spectra in the spectrum comparison view, particularly on macOS.

• a central spectral region can now be masked in the Range Selection preprocessing step, which facilitates automated image formation of Brillouin scattering datasets.

• data can now be (reversibly) scaled before statistical denoising to denoise spectral datasets with signals that span many orders of magnitude.

• the background color of 2D or 3D graphs can now be changed:

  • for the current graph using the right-click context menu

  • in Preferences

• improvements to spectral series export.

• added an NMF initialization option to MCR decomposition.

1.2.3.2. Bug Fixes

• improved support of older .smd files.

• trace names are now properly preserved during .mdt or .hdf5 spectra export

• the Save figures with transparent background setting is now honored when exporting images to the system pasteboard

1.2.4. SMDExplorer 1.0.2 (‘True Blue’)

1.2.4.1. New features

• plot images can now be copied to the system clipboard using the standard system copy keyboard shortcut Ctrl-C (⌘-C on macOS). This requires the plot to have focus, which can be achieved by simply clicking into the plot - focus is indicated by a black border. To copy plot data as text, please use the Copy Data toolbar button.

• single spectra can now be manually or automatically scaled / offset for better comparison.

• spectra in the compare spectra window can now be manually scaled and offset for better comparison

• the z-direction of surface plots can now be inverted to accommodate mappings where the key feature of interest manifests itself as a minimum in intensity

• improvements to image export of 3D mappings:

  • added the option to export 3D-mappings with (interpolated) cubic voxels

  • the currently displayed slice is now indicated using a label when exporting 3D-data as an animation or montage

  • image export is now also available for 3D mappings obtained from fits

• added the Translucency (no depth) blend mode for 3D volumetric display.

• volumetric display of logarithmically scaled data

• Smooth Factor Analysis denoising, which combines smoothing and PCA-based statistical denoising

• improvements to 2D projection volume animations

1.2.4.2. Bug Fixes

• extraneous whitespace is now excluded when copying figures to the system clipboard.

• the layer slider in the 3D mappings window now works properly for non-integer steps.

• performance improvements to point cloud display.

1.2.5. SMDExplorer 1.0.1 (‘Lucky Star’)

1.2.5.1. New features

• added version information to the Windows release. Version information is available by right-clicking the SMDExplorer executable and selecting Properties ‣ Details.

• preprocessing steps can be reordered by dragging the items in the preprocessing methods list.

• logarithmic scaling can now be used on vertical axes.

• axes can now be easily inverted using a checkbox in the Axis Dialog. This was possible before (but tedious) by manually swapping the minimum and maximum axis limits.

• added the option to whiten the data before decomposition.

• figures are now saved using a transparent background. This can be switched off in Preferences.

• improved display of three-dimensional data. Please see the section 3D Plots for details.

• spectra can now be scaled to unit area or between 0 and 1 (see Normalization).

• color scales and ranges can now be adjusted individually in two-dimensional overlay views

• improved surface plots for two-dimensional topographical intensity maps (Windows only)

• the result of a K-Means clustering operation can now be exported as a spectral series or a spectral database for separate analysis of the spectra found in a cluster. Please note that this requires K-Means clustering to be performed in Label mode.

• downsampling can now be used to compute a single average spectrum from a one-dimensional scan, for example the average spectrum of a time series. Alternatively, this can be achieved by switching to range selection mode and selecting the entire spectral range in the mapping pane to compute the mean spectrum. Note that downsampling gives access to the median and maximum-projected spectrum (maximum intensity per channel) in addition to the mean spectrum as well.

• the spatial / temporal dimensions of datasets can now be cropped to regions of interest

• round-tripping for .mdt database files as well as export to .mdt files from graphs is now supported, improving interoperability with the Nanofinder software.

• in addition to two-dimensional spectrograms and waterfall plots, SMDExplorer now also supports the display of spectral scans as spectral surface plots

• readout and display of acquisition parameters from .smd files.

• line profile analysis and surface plots are now accessible via the right-click context menu in all two-dimensional spectral mappings.

• particle analysis

1.2.5.2. Bug Fixes

• renaming spectra in the Spectra Comparison View now works properly.

• improved drawing performance in the preprocessing window when using SMDExplorer in single-spectra mode.

• improved preservation of scale information when exporting mappings to .hdf5 or .tiff.

• fixed an issue when importing a very old version of the .smd file format

• fixed an issue when importing .mdt spectral databases containing image data

• fixed a bug when exporting a .hdf5 spectra database for spectra with the same name the same name.

• graph export to .svg and .webp now works properly.

• improved navigation in the decomposition overlay view.

• fixed a logic error when downsampling three-dimensional data

• overlay display now works when using cluster labels after K-means clustering