OpenSpecy-package: OpenSpecy: Analyze, Process, Identify, and Share Raman and...
In OpenSpecy: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
OpenSpecy-package R 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, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1021/acs.analchem.1c00123")}). With read_any(), Open Specy provides a single function for reading individual, batch, or map spectral data files like .asp, .csv, .jdx, .spc, .spa, .0, and .zip. process_spec() simplifies processing spectra, including smoothing, baseline correction, range restriction and flattening, intensity conversions, wavenumber alignment, and min-max normalization. Spectra can be identified in batch using an onboard reference library (Cowger et al. 2020, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1177/0003702820929064")}) using match_spec(). A Shiny app is available via run_app() or online at https://openanalysis.org/openspecy/.
Author(s)
Maintainer: Win Cowger wincowger@gmail.com (ORCID) [data contributor]
Authors:
Zacharias Steinmetz z.steinmetz@rptu.de (ORCID)
Nick Leong (ORCID)
Andrea Faltynkova (ORCID) [data contributor]
Hannah Sherrod (ORCID)
Other contributors:
Andrew B 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]
Mary C Norris [contributor]
Christine M Knauss (ORCID) [contributor]
Aleksandra Karapetrova (ORCID) [contributor, data contributor, reviewer]
Vesna Teofilovic (ORCID) [contributor]
Laura A. T. Markley (ORCID) [contributor]
Shreyas Patankar [contributor, data contributor]
Rachel Kozloski (ORCID) [contributor, data contributor]
Samiksha Singh [contributor]
Katherine Lasdin [contributor]
Cristiane Vidal (ORCID) [contributor]
Clare Murphy-Hagan (ORCID) [contributor]
Philipp Baumann info@spectral-cockpit.space (ORCID) [contributor]
Pierre Roudier [contributor]
National Renewable Energy Laboratory [funder]
Possibility Lab [funder]
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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1177/0003702820923993")}.
Cowger W, Gray A, 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.
\Sexpr[results=rd]{tools:::Rd_expr_doi("10.1177/0003702820929064")}.
Cowger, W (2023). “Library data.” OSF. \Sexpr[results=rd]{tools:::Rd_expr_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.
\Sexpr[results=rd]{tools:::Rd_expr_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. \Sexpr[results=rd]{tools:::Rd_expr_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.
\Sexpr[results=rd]{tools:::Rd_expr_doi("10.1366/000370207782597003")}.
See Also
Useful links:
OpenSpecy documentation built on Sept. 14, 2024, 9:07 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| OpenSpecy-package | R 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, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1021/acs.analchem.1c00123")}). With read_any(), Open Specy provides a single function for reading individual, batch, or map spectral data files like .asp, .csv, .jdx, .spc, .spa, .0, and .zip. process_spec() simplifies processing spectra, including smoothing, baseline correction, range restriction and flattening, intensity conversions, wavenumber alignment, and min-max normalization. Spectra can be identified in batch using an onboard reference library (Cowger et al. 2020, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1177/0003702820929064")}) using match_spec(). A Shiny app is available via run_app() or online at https://openanalysis.org/openspecy/.
Author(s)
Maintainer: Win Cowger wincowger@gmail.com (ORCID) [data contributor]
Authors:
Zacharias Steinmetz z.steinmetz@rptu.de (ORCID)
Nick Leong (ORCID)
Andrea Faltynkova (ORCID) [data contributor]
Hannah Sherrod (ORCID)
Other contributors:
Andrew B 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]
Mary C Norris [contributor]
Christine M Knauss (ORCID) [contributor]
Aleksandra Karapetrova (ORCID) [contributor, data contributor, reviewer]
Vesna Teofilovic (ORCID) [contributor]
Laura A. T. Markley (ORCID) [contributor]
Shreyas Patankar [contributor, data contributor]
Rachel Kozloski (ORCID) [contributor, data contributor]
Samiksha Singh [contributor]
Katherine Lasdin [contributor]
Cristiane Vidal (ORCID) [contributor]
Clare Murphy-Hagan (ORCID) [contributor]
Philipp Baumann info@spectral-cockpit.space (ORCID) [contributor]
Pierre Roudier [contributor]
National Renewable Energy Laboratory [funder]
Possibility Lab [funder]
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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1177/0003702820923993")}.
Cowger W, Gray A, 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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1177/0003702820929064")}.
Cowger, W (2023). “Library data.” OSF. \Sexpr[results=rd]{tools:::Rd_expr_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. \Sexpr[results=rd]{tools:::Rd_expr_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. \Sexpr[results=rd]{tools:::Rd_expr_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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1366/000370207782597003")}.
See Also
Useful links:
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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