Spectral-Cockpit: “Scale-up chemical diagnostics”:

• FLOSS: Community projects:
  • moving to https://codefloe.com/spectral-cockpit
  • this presentation: https://codefloe.com/spectral-cockpit/presentations
• Analytics Platform: automation for research labs and commercial services. Holistic consulting.

Spectral-Cockpit: Where it started?

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Automation starts in the lab and with data collection

Bruker Alpha mid-infrared spectrometer | soil samples in plate for Bruker Vertex 70

• Getting data out of spectra is often unclean
  • Binary formats can be proprietary
  • Or hacky workarounds and old-fashioned formats
• Spectra contain a lot of useful information on quality and they also contain single channel spectra
• Scale up spectral diagnostics and build spectral libraries

Meet {opusreader2}

• Read OPUS binary files from Fourier-Transform Infrared (FT-IR) spectrometers of the company Bruker Optics GmbH & Co. in base R
  • The Bruker corporation produces reliable instruments
  • However, there is no official documentation for the OPUS file format, making it proprietary
  • Import OPUS measurement data and parameters with ease
• https://codefloe.com/spectral-cockpit/opusreader2/

Meet {opusreader2}

• Organizations and projects using {opusreader2}:
  • CSIRO: https://github.com/csiro/soilspec.format
  • ETH Zürich: Sustainable Agroecosystems and Soil Resources labs
  • Open Soil Spectral Library: https://docs.soilspectroscopy.org/soilspec.html#software
  • OpenSpecy: https://www.plastiverse.org/tools/openspecy
  • Kompetenzzentrum Boden (KOBO)
• Passes all checks, CRAN submission today

Meet {opusreader2}

https://opusreader2.spectral-cockpit.com

{opusreader2}: Getting started

if (!require("remotes")) install.packages("remotes")
remotes::install_git("https://codefloe.com/spectral-cockpit/opusreader2")

• Read example files shipped with the package

library("opusreader2")

dsn <- opus_test_dsn()
data <- read_opus(dsn = dsn)
print(data)

╔==============================================================================╗ 
                      OPUS collection with 5 spectra                       
╚==============================================================================╝ 
Measurement metadata:
* date-time range (UTC): [2015-11-06 13:39:33 , 2021-11-09 14:57:44]
 
* data blocks (#spectra) ------------------------------------------------------- 
   ab (4);   ab_no_atm_comp (2);   ig_ref (3);   ig_sample (3); 
  match (1);   match_2_chn (1);   refl_no_atm_comp (1);   sc_ref (5); 
  sc_sample (5);
 
* parameter blocks (#spectra) -------------------------------------------------- 
   ab_data_param (4);   ab_no_atm_comp_data_param (2);   acquisition (5); 
  acquisition_ref (5);   fourier_transformation (5); 
  fourier_transformation_ref (5);   ig_ref_data_param (3); 
  ig_sample_data_param (3);   info_block (3);   instrument (5); 
  instrument_ref (5);   lab_and_process_param_processed (3); 
  lab_and_process_param_raw (2);   match_2_chn_data_param (1); 
  match_data_param (1);   me_test_report_ab (1);   optics (5); 
  optics_ref (5);   quant_report_ab (1);   quant_report_refl (1); 
  refl_no_atm_comp_data_param (1);   sample (5);   sc_ref_data_param (5); 
  sc_sample_data_param (5);

{opusreader2}

Plot the data

x <- rev(data[[1]]$ab$wavenumbers)
y <- rev(data[[1]]$ab$data)

# first spectrum in the collection
plot(x = x, y = y, type = "l", xlab = "Wavenumber [1/cm]", ylab = "Absorbance (a.u.)", xlim = range(x), ylim = range(y))

Resources

Spectroscopy research

• Baumann, P. (2021). Scaling-up Soil Quality Assessments: Efficient Infrared-spectroscopic Workflows across Space and Time [Doctoral Thesis, ETH Zurich]. https://doi.org/10.3929/ethz-b-000549011

• Baumann, P., Helfenstein, A., Gubler, A., Keller, A., Meuli, R. G., Wächter, D., Lee, J., Viscarra Rossel, R., & Six, J. (2021). Developing the Swiss mid-infrared soil spectral library for local estimation and monitoring. SOIL, 7(2), 525–546. https://doi.org/10.5194/soil-7-525-2021

• Baumann, P., Lee, J., Behrens, T., Biswas, A., Six, J., McLachlan, G., & Viscarra Rossel, R. A. (2022). Modelling soil water retention and water-holding capacity with visible–near-infrared spectra and machine learning. European Journal of Soil Science, 73(2), e13220. https://doi.org/10.1111/ejss.13220

Related software and applications

• Baumann P, Knecht T, Roudier P (2026). opusreader2: Read Spectroscopic Data from Bruker OPUS Binary Files. R package version 0.6.6, https://opusreader2.spectral-cockpit.codefloe.page/

Projects using {opusreader2}

• Open Soil Spectral Library (OSSL): Building reproducible soil calibration models through open development and community engagement

• CSIRO: https://github.com/csiro/soilspec.format