OpenSpecy-package: OpenSpecy: Analyze, Process, Identify, and Share Raman and...

OpenSpecy-packageR Documentation

OpenSpecy: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra

Description

Raman and (FT)IR spectral analysis tool for plastic particles and other environmental samples (Cowger et al. 2021, doi: 10.1021/acs.analchem.1c00123). Supported features include reading spectral data files (.asp, .csv, .jdx, .spc, .spa, .0), Savitzky-Golay smoothing of spectral intensities with smooth_intens(), correcting background noise with subtr_bg() in accordance with Zhao et al. (2007) doi: 10.1366/000370207782597003, and identifying spectra using an onboard reference library (Cowger et al. 2020, doi: 10.1177/0003702820929064). Analyzed spectra can be shared with the Open Specy community. A Shiny app is available via run_app() or online at https://openanalysis.org/openspecy/.

Author(s)

Maintainer: Win Cowger wincowger@gmail.com (ORCID)

Authors:

Other contributors:

  • Andrew Gray (ORCID) [contributor]

  • Hannah Hapich (ORCID) [contributor]

  • Jennifer Lynch (ORCID) [contributor, data contributor]

  • Hannah De Frond (ORCID) [contributor, data contributor]

  • Keenan Munno (ORCID) [contributor, data contributor]

  • Chelsea Rochman (ORCID) [contributor, data contributor]

  • Sebastian Primpke (ORCID) [contributor, data contributor]

  • Orestis Herodotou [contributor, data contributor]

References

Chabuka BK, Kalivas JH (2020). “Application of a Hybrid Fusion Classification Process for Identification of Microplastics Based on Fourier Transform Infrared Spectroscopy.” Applied Spectroscopy, 74(9), 1167–1183. doi: 10.1177/0003702820923993.

Cowger W, Gray A, Christiansen SH, Christiansen SH, Christiansen SH, De Frond H, Deshpande AD, Hemabessiere L, Lee E, Mill L, et al. (2020). “Critical Review of Processing and Classification Techniques for Images and Spectra in Microplastic Research.” Applied Spectroscopy, 74(9), 989–1010. doi: 10.1177/0003702820929064.

Cowger, W (2021). “Library data.” OSF. doi: 10.17605/OSF.IO/X7DPZ.

Cowger W, Steinmetz Z, Gray A, Munno K, Lynch J, Hapich H, Primpke S, De Frond H, Rochman C, Herodotou O (2021). “Microplastic Spectral Classification Needs an Open Source Community: Open Specy to the Rescue!” Analytical Chemistry, 93(21), 7543–7548. doi: 10.1021/acs.analchem.1c00123.

Primpke S, Wirth M, Lorenz C, Gerdts G (2018). “Reference Database Design for the Automated Analysis of Microplastic Samples Based on Fourier Transform Infrared (FTIR) Spectroscopy.” Analytical and Bioanalytical Chemistry, 410(21), 5131–5141. doi: 10.1007/s00216-018-1156-x.

Savitzky A, Golay MJ (1964). “Smoothing and Differentiation of Data by Simplified Least Squares Procedures.” Analytical Chemistry, 36(8), 1627–1639.

Zhao J, Lui H, McLean DI, Zeng H (2007). “Automated Autofluorescence Background Subtraction Algorithm for Biomedical Raman Spectroscopy.” Applied Spectroscopy, 61(11), 1225–1232. doi: 10.1366/000370207782597003.

See Also

Useful links:


OpenSpecy documentation built on July 6, 2022, 5:07 p.m.