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Instrukcje - Narodowe Centrum Promieniowania Synchrotronowego SOLARIS

Beamlines

Manuals and software

Manuals:

A printed manual for carrying out measurements in various modes, prepared by the producer of the microscope, is available in the laboratory. Using link below, you can download the instruction prepared by the beamline scientists. The manuals include the steps of measurements in the transmission, transflection, and ATR modes with the FPA and MCT detector.

  1. Link to manual for transmission, reflection, and transflection mode with FPA and MCT.
  2. Link to anual for ATR with FPA and MCT.

Software:

The producer of the microscope, Bruker, provides the OPUS software for measurements and initial spectra evaluation. It is also possible to run a "macro" to control the microscope. The software allows you to save data in the form of interferograms or spectra in various formats: ENVI, table of data points, MATLAB 4 or 5, and others. 
The producer provides the OPUS Viewer program for free, with which you can open OPUS files without the possibility of data processing, only viewing them.
Data obtained from microscopic measurements (mapping or imaging) are hyperspectral and three-dimensional.
 
Suggestions of software for data analysis:
  • The CytoSpec program is dedicated to multidimensional imaging of spectroscopic data. It allows the processing of data using statistical methods (chemometrics) and machine learning, using spectral and spatial information. It is one of the programs dedicated to the processing of three-dimensional, hyperspectral data matrices from infrared imaging experiments. Link to the program.
  • Quasar is an open-source collection of spectroscopic data analysis toolboxes extending the Orange machine learning and data visualization suite. Link to the program. 
  • Programs dedicated to scientific (numerical) calculations and data visualization: MATLAB, GNU Octave, and others.

Performing measurements:

The s-SNOM/AFM-IR microscope is controlled via manufacturer-supplied software (neaSCAN). A printed copy of the microscope's operating manual is available on-site.

Data analysis:

Data collected during s-SNOM/AFM-IR measurements are saved in .gsf and .gwy formats for imaging measurements, and in .txt format for spectral measurements. The recommended software for image visualization and analysis is the free software Gwyddion. A guide containing information on data access, file structure, and suggestions for data viewing and analysis is available via the active link.