Technical note: &bdquo;U-Th Analysis&rdquo; &ndash; an open-source software dedicated to MCICPMS U-series-data treatment and evaluation

Kerber, Inga Kristina; Kontor, Fabian; Warken, Sophie; Frank, Norbert

doi:https://doi.org/10.5194/egusphere-2024-1788

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https://doi.org/10.5194/egusphere-2024-1788

Preprints

25 Jun 2024

| 25 Jun 2024

Technical note: „U-Th Analysis” – an open-source software dedicated to MCICPMS U-series-data treatment and evaluation

Inga Kristina Kerber, Fabian Kontor, Sophie Warken, and Norbert Frank

Abstract. We present our standalone data analysis application for ²³⁰Th/U dating on multi-collector inductively coupled plasma mass spectrometers (MC-ICP-MS). The Python-based algorithm is equipped with a graphical user interface (GUI) and comprises raw data treatment, corrections, age calculation, and error estimation. Our underlying measurement protocol employs a combination of Faraday cups (FC) and secondary electron multipliers (SEM), and the software allows for different detector layouts for the measurement of the least abundant isotopes ²³⁴U, ²³⁰Th and ²²⁹Th. We especially focus on features that ensure reproducibility and enable user-friendly reanalysis of measurements such as customized calculation constants with templates. Result files are saved automatically and contain all relevant settings used. Eventually, we demonstrate the relevance of adequate data outlier treatment and generally recommend using the median instead of the mean of calculated ratios. The performance of our evaluation software is demonstrated by a case study from a Puerto Rican stalagmite with growth phases from modern to 40 ka old. The majority of the obtained ages reaches uncertainties in the range of 0.3–0.6 %, underlining the capability of our measurement protocol.

Received: 12 Jun 2024 – Discussion started: 25 Jun 2024

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06 Jan 2025

Technical note: “U–Th Analysis” – open-source software dedicated to MC-ICP-MS U-series data treatment and evaluation

Inga Kristina Kerber, Fabian Kontor, Aaron Mielke, Sophie Warken, and Norbert Frank

Geochronology, 7, 1–13, https://doi.org/10.5194/gchron-7-1-2025,https://doi.org/10.5194/gchron-7-1-2025, 2025

Short summary

Inga Kristina Kerber, Fabian Kontor, Sophie Warken, and Norbert Frank

Interactive discussion

Status: closed

RC1:
'Comment on egusphere-2024-1788', Anonymous Referee #1, 14 Aug 2024

GENERAL COMMENTS
The preprint by Kerber et al. presents an algorithm designed for handling raw data treatment, corrections, age calculation, and error estimation for ²³⁰Th/U dating using multi-collector inductively coupled plasma mass spectrometers (MC-ICP-MS). The algorithm is coded in Python and also provided as an open-source graphical user interface (GUI) software. A case study of a stalagmite from Larga Cave, Puerto Rico, is used to demonstrate how the algorithm works and its ability to calculate ages with uncertainties as low as 0.3-0.6%.
The intention of the algorithm is to simplify the data reduction and age calculation in a more reproducible and standardized manner. Discussion of data treatment includes corrections for various measurement artifacts such as peak tailing and hydride interference, and the importance of outlier correction. The preprint makes a case for the use of medians instead of means for more accurate data analysis. In addition, the preprint discusses the significance of initial ²³⁰Th correction and shows how easily the initial (²³⁰Th/²³²Th) activity ratio can be adjusted in the GUI to assess or accomplish Th correction.
Different detector arrangements used in different laboratories can already be accommodated in the GUI, but expert users can also modify the code if their detector arrangement is not supported. Importantly, users of the ²³⁰Th/U dating technique who are not involved in the measurements and production of the data can easily become involved in the data treatment and age calculation. The GUI is well-designed with a workflow that is easier to follow, and the preprint adequately describes how to use the GUI and make changes to constants or assumptions. Data treatment and age calculations can be time-consuming and external users can wait a long time before receiving results of their submitted samples, but the GUI can assist many labs with relegating the data treatment and age calculation steps to the external users, and thereby expedite the finalization of results.

SPECIFIC COMMENTS
It is not explicitly stated that the GUI is for handling data from ThermoFisher Neptune instruments only or how data from other instruments can be handled. This would be beneficial to users of the ²³⁰Th/U dating method with data from other instruments.

TECHNICAL CORRECTIONS
Line 51: The use of "(i)" is confusing since no list is provided.
Line 62: “initial Thorium” should be “initial Th” for consistency within the same sentence and entire document.
Line 259: In this section “3.3 Analysis tab” the numbers in parentheses are not consistent with Figure 3. For example, line 265 makes reference to (3) for “Start Analysis” and (4) for presentation of the results, but there is no (3) and (4) in Figure 3.
Line 263: The exemplary Excel file for the weight table provided in the supplementary data should have its sheet names and column headers translated from Deutsche to English for accessibility.
Line 310: Delete the first “as well as the algorithms Stalage, copRa and bchron linear interpolation”
Line 316: Caption for supplementary Figure S3 has “223Th” instead of “232Th”
Line 353: “which is much stronger influenced by” please revise. Strongly instead?
Line 373: “this correction particularly” is missing “is”

Citation: https://doi.org/10.5194/egusphere-2024-1788-RC1
- AC2: 'Reply on RC1', Norbert Frank, 09 Sep 2024
  
  The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2024/egusphere-2024-1788/egusphere-2024-1788-AC2-supplement.pdf
  
  Citation: https://doi.org/10.5194/egusphere-2024-1788-AC2
RC2:
'Comment on egusphere-2024-1788', Anonymous Referee #2, 17 Aug 2024
This paper presents a Python-based program “U-Th Analysis” designed for U-Th isotopic data analysis for MC-ICPMS U-series dating. The program has a friendly graphical user interface and is open for the source code, which can be modified according to the measurement methods. This program comprises many automatic functions: e.g., to calculate U and Th tailing effects, identify outliers in isotopic ratios, correct for initial 230Th contamination, as well as to load and save data. I support to accept this paper for publication, as a transparent data treatment algorithms is desired for each of dating laboratories.
I have a few comments:
U-Th isotopes can be measured using MC-ICPMS with different methods, and in many labs, the two elements were measured separately. In the Conclusion of this study, it was mentioned that the U-Th were measured simultaneously. I think the isotopic measurement method should be clarified before describing the program, probably in the section of “2.2. Chemical preparation and instrumentation”.

If I understand well, the “Input” tab performs corrections of blank, tailing, and hydride, the “Inspect” tab filters the outliers from isotopic ratios, and the “Analysis” tab calculates the U-series age and corrects for initial 230Th contaminations. The combination of FC and SEM was used for U-Th measurements, so, I want to know how the SEM/FC yield is corrected, and how mass fractionation is corrected, and if the uncertainties of the two factors are considered in the program.

In line 211, it was mentioned that the instrument background is measured between all sample and standard measurements for 70 s. Is the background measured on SEM by peak-jumping or by the combination of SEM and FC? For the blank correction, are the outliers in the blank measurements filtered.

A few typos:
Line 30: The “manifold in geochemistry, archaeology, and climate science” was repeated.

Line 192: What is the “GUI (10)”?

Line 205: It should be “Thorium tailing”.

Line 323; It should be “Figure 5”.
Citation: https://doi.org/10.5194/egusphere-2024-1788-RC2
- AC1: 'Reply on RC2', Norbert Frank, 09 Sep 2024
  
  The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2024/egusphere-2024-1788/egusphere-2024-1788-AC1-supplement.pdf
  
  Citation: https://doi.org/10.5194/egusphere-2024-1788-AC1

Interactive discussion

Status: closed

RC1:
'Comment on egusphere-2024-1788', Anonymous Referee #1, 14 Aug 2024

GENERAL COMMENTS
The preprint by Kerber et al. presents an algorithm designed for handling raw data treatment, corrections, age calculation, and error estimation for ²³⁰Th/U dating using multi-collector inductively coupled plasma mass spectrometers (MC-ICP-MS). The algorithm is coded in Python and also provided as an open-source graphical user interface (GUI) software. A case study of a stalagmite from Larga Cave, Puerto Rico, is used to demonstrate how the algorithm works and its ability to calculate ages with uncertainties as low as 0.3-0.6%.
The intention of the algorithm is to simplify the data reduction and age calculation in a more reproducible and standardized manner. Discussion of data treatment includes corrections for various measurement artifacts such as peak tailing and hydride interference, and the importance of outlier correction. The preprint makes a case for the use of medians instead of means for more accurate data analysis. In addition, the preprint discusses the significance of initial ²³⁰Th correction and shows how easily the initial (²³⁰Th/²³²Th) activity ratio can be adjusted in the GUI to assess or accomplish Th correction.
Different detector arrangements used in different laboratories can already be accommodated in the GUI, but expert users can also modify the code if their detector arrangement is not supported. Importantly, users of the ²³⁰Th/U dating technique who are not involved in the measurements and production of the data can easily become involved in the data treatment and age calculation. The GUI is well-designed with a workflow that is easier to follow, and the preprint adequately describes how to use the GUI and make changes to constants or assumptions. Data treatment and age calculations can be time-consuming and external users can wait a long time before receiving results of their submitted samples, but the GUI can assist many labs with relegating the data treatment and age calculation steps to the external users, and thereby expedite the finalization of results.

SPECIFIC COMMENTS
It is not explicitly stated that the GUI is for handling data from ThermoFisher Neptune instruments only or how data from other instruments can be handled. This would be beneficial to users of the ²³⁰Th/U dating method with data from other instruments.

TECHNICAL CORRECTIONS
Line 51: The use of "(i)" is confusing since no list is provided.
Line 62: “initial Thorium” should be “initial Th” for consistency within the same sentence and entire document.
Line 259: In this section “3.3 Analysis tab” the numbers in parentheses are not consistent with Figure 3. For example, line 265 makes reference to (3) for “Start Analysis” and (4) for presentation of the results, but there is no (3) and (4) in Figure 3.
Line 263: The exemplary Excel file for the weight table provided in the supplementary data should have its sheet names and column headers translated from Deutsche to English for accessibility.
Line 310: Delete the first “as well as the algorithms Stalage, copRa and bchron linear interpolation”
Line 316: Caption for supplementary Figure S3 has “223Th” instead of “232Th”
Line 353: “which is much stronger influenced by” please revise. Strongly instead?
Line 373: “this correction particularly” is missing “is”

Citation: https://doi.org/10.5194/egusphere-2024-1788-RC1
- AC2: 'Reply on RC1', Norbert Frank, 09 Sep 2024
  
  The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2024/egusphere-2024-1788/egusphere-2024-1788-AC2-supplement.pdf
  
  Citation: https://doi.org/10.5194/egusphere-2024-1788-AC2
RC2:
'Comment on egusphere-2024-1788', Anonymous Referee #2, 17 Aug 2024
This paper presents a Python-based program “U-Th Analysis” designed for U-Th isotopic data analysis for MC-ICPMS U-series dating. The program has a friendly graphical user interface and is open for the source code, which can be modified according to the measurement methods. This program comprises many automatic functions: e.g., to calculate U and Th tailing effects, identify outliers in isotopic ratios, correct for initial 230Th contamination, as well as to load and save data. I support to accept this paper for publication, as a transparent data treatment algorithms is desired for each of dating laboratories.
I have a few comments:
U-Th isotopes can be measured using MC-ICPMS with different methods, and in many labs, the two elements were measured separately. In the Conclusion of this study, it was mentioned that the U-Th were measured simultaneously. I think the isotopic measurement method should be clarified before describing the program, probably in the section of “2.2. Chemical preparation and instrumentation”.

If I understand well, the “Input” tab performs corrections of blank, tailing, and hydride, the “Inspect” tab filters the outliers from isotopic ratios, and the “Analysis” tab calculates the U-series age and corrects for initial 230Th contaminations. The combination of FC and SEM was used for U-Th measurements, so, I want to know how the SEM/FC yield is corrected, and how mass fractionation is corrected, and if the uncertainties of the two factors are considered in the program.

In line 211, it was mentioned that the instrument background is measured between all sample and standard measurements for 70 s. Is the background measured on SEM by peak-jumping or by the combination of SEM and FC? For the blank correction, are the outliers in the blank measurements filtered.

A few typos:
Line 30: The “manifold in geochemistry, archaeology, and climate science” was repeated.

Line 192: What is the “GUI (10)”?

Line 205: It should be “Thorium tailing”.

Line 323; It should be “Figure 5”.
Citation: https://doi.org/10.5194/egusphere-2024-1788-RC2
- AC1: 'Reply on RC2', Norbert Frank, 09 Sep 2024
  
  The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2024/egusphere-2024-1788/egusphere-2024-1788-AC1-supplement.pdf
  
  Citation: https://doi.org/10.5194/egusphere-2024-1788-AC1

Peer review completion

AR: Author's response | RR: Referee report | ED: Editor decision | EF: Editorial file upload

ED: Publish subject to minor revisions (further review by editor) (18 Sep 2024) by Pieter Vermeesch

The two reviewers have only minor comments on your Technical Note, which you have adequately addressed in your response letters. I am therefore happy to recommend publication of your paper in Geochronology pending these changes. However, I would also like you to address a few additional points which I have found after reading the paper myself:

1. Lines 29 and 30 contain duplicate sentences and use the word “manifold” instead of “manyfold”.

2. Equations 1 -3 are unnecessary. Standard deviation, standard error, interquartile range and median absolute deviation are commonly used terms that do not need explicit definitions in a paper of this kind.

3. Line 245 states that your software uses means of ratios. This treatment has some undesirable statistical properties (as detailed by, for example, Ogliore, NIM-B, 2011 and McLean et al., G-Cubed, 2016). It would be useful to offer your users the ratio of the means as an alternative solution.

4. Line 297: What does “dft” stand for?

5. Sections 4 and 5.3 can be shortened. People will read your technical note to learn more about your software. Most of them probably won’t care so much about its application to Speleothem B1. As far as I can tell, Figures 4 and 5 were not generated by your software. I think they can be moved to the supplement.

6. Line 338 suggests that means should be replaced by medians. However, Section 3.3 says that the software uses means (of ratios). Which is correct?

7. Line 339 states that outlier rejection is done using box plots. Can you clarify how this works? The convention is that box plots define outliers as being more than 1.5 IQR above or below the median. Did you follow this definition?

8. According to line 351: “The default method (2 standard deviation) does not remove all the systematic outliers”. What do you mean with “default method”? A 2 sigma cutoff is a very poor outlier detection criterion, as it rejects 5% non-outliers. This is called a “type-1” error in statistics. If your software includes a 2-sigma criterion, then please remove it.

9. Line 384: Supplementary table S1 uses three widely different initial 230Th/232Th ratios (0.75, 11 and 75). One of these ([230Th/232Th] = 11) is based on drip waters. How were the other estimates obtained. Lines 62-71 mention isochrons and independent age constraints as alternative means of estimating the detrital component. Did you use those? Does your software perform isochron regression? If so, does it implement the Ludwig and Titterington (1994) algorithm. Some more details would be useful here.

10. Although the Windows executable is useful, it would also be helpful if your code would work on other operating systems as well. However, when running your Python code on my computer (Ubuntu 22.04), I get the following error message:

Traceback (most recent call last):
File "/home/pvermees/temp/UTh_Analysis/main.py", line 259, in
GUI = Window()
File "/home/pvermees/temp/UTh_Analysis/main.py", line 40, in __init__
self.inputTab = InputTabWidget(self, self.ratioBuilder)
File "/home/pvermees/temp/UTh_Analysis/InputTabWidget.py", line 35, in __init__
self.initOverviewBox()
File "/home/pvermees/temp/UTh_Analysis/InputTabWidget.py", line 509, in initOverviewBox
self.uTailTable.setVerticalScrollMode(QtGui.QAbstractItemView.ScrollPerPixel)
AttributeError: module 'pyqtgraph.Qt.QtGui' has no attribute 'QAbstractItemView'

Please feel free to email me if you need further information to fix this problem, or if you have any questions about this decision letter.

Pieter Vermeesch

Hide

AR by Norbert Frank on behalf of the Authors (11 Oct 2024) Author's response Author's tracked changes Manuscript

ED: Publish subject to minor revisions (further review by editor) (21 Oct 2024) by Pieter Vermeesch

AR by Norbert Frank on behalf of the Authors (04 Nov 2024) Author's response Author's tracked changes Manuscript

ED: Publish as is (05 Nov 2024) by Pieter Vermeesch

ED: Publish as is (05 Nov 2024) by Klaus Mezger (Editor)

AR by Norbert Frank on behalf of the Authors (06 Nov 2024) Author's response Manuscript

Journal article(s) based on this preprint

06 Jan 2025

Technical note: “U–Th Analysis” – open-source software dedicated to MC-ICP-MS U-series data treatment and evaluation

Inga Kristina Kerber, Fabian Kontor, Aaron Mielke, Sophie Warken, and Norbert Frank

Geochronology, 7, 1–13, https://doi.org/10.5194/gchron-7-1-2025,https://doi.org/10.5194/gchron-7-1-2025, 2025

Short summary

Inga Kristina Kerber, Fabian Kontor, Sophie Warken, and Norbert Frank

Supplement

https://doi.org/10.5194/egusphere-2024-1788-supplement

Model code and software

UTh Data Analysis Fabian Kontor and Inga Kristina Kerber https://github.com/EnvArchivesHD/UTh_Analysis

Inga Kristina Kerber, Fabian Kontor, Sophie Warken, and Norbert Frank

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A standalone data analysis application for Th/U dating on multi-collector inductively coupled plasma mass spectrometers features a Python-based algorithm with a graphical user interface. It handles data treatment, corrections, age calculus, and error estimation and supports various detector layouts including Faraday and electron multiplier detectors. Key features include reproducibility, user-friendly reanalysis, and automated data storage. A case study demonstrated the software’s performance.


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