-
Notifications
You must be signed in to change notification settings - Fork 21
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #4928 from openjournals/joss.05686
Merging automatically
- Loading branch information
Showing
6 changed files
with
1,042 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,335 @@ | ||
<?xml version="1.0" encoding="UTF-8"?> | ||
<doi_batch xmlns="http://www.crossref.org/schema/5.3.1" | ||
xmlns:ai="http://www.crossref.org/AccessIndicators.xsd" | ||
xmlns:rel="http://www.crossref.org/relations.xsd" | ||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" | ||
version="5.3.1" | ||
xsi:schemaLocation="http://www.crossref.org/schema/5.3.1 http://www.crossref.org/schemas/crossref5.3.1.xsd"> | ||
<head> | ||
<doi_batch_id>20240119T094236-3030dc3f48b6fad840061c6afc1aa47447a74304</doi_batch_id> | ||
<timestamp>20240119094236</timestamp> | ||
<depositor> | ||
<depositor_name>JOSS Admin</depositor_name> | ||
<email_address>[email protected]</email_address> | ||
</depositor> | ||
<registrant>The Open Journal</registrant> | ||
</head> | ||
<body> | ||
<journal> | ||
<journal_metadata> | ||
<full_title>Journal of Open Source Software</full_title> | ||
<abbrev_title>JOSS</abbrev_title> | ||
<issn media_type="electronic">2475-9066</issn> | ||
<doi_data> | ||
<doi>10.21105/joss</doi> | ||
<resource>https://joss.theoj.org</resource> | ||
</doi_data> | ||
</journal_metadata> | ||
<journal_issue> | ||
<publication_date media_type="online"> | ||
<month>01</month> | ||
<year>2024</year> | ||
</publication_date> | ||
<journal_volume> | ||
<volume>9</volume> | ||
</journal_volume> | ||
<issue>93</issue> | ||
</journal_issue> | ||
<journal_article publication_type="full_text"> | ||
<titles> | ||
<title>PATATO: a Python photoacoustic tomography analysis | ||
toolkit</title> | ||
</titles> | ||
<contributors> | ||
<person_name sequence="first" contributor_role="author"> | ||
<given_name>Thomas R.</given_name> | ||
<surname>Else</surname> | ||
<ORCID>https://orcid.org/0000-0002-2652-4190</ORCID> | ||
</person_name> | ||
<person_name sequence="additional" | ||
contributor_role="author"> | ||
<given_name>Janek</given_name> | ||
<surname>Gröhl</surname> | ||
<ORCID>https://orcid.org/0000-0002-5332-4856</ORCID> | ||
</person_name> | ||
<person_name sequence="additional" | ||
contributor_role="author"> | ||
<given_name>Lina</given_name> | ||
<surname>Hacker</surname> | ||
<ORCID>https://orcid.org/0000-0001-5160-0952</ORCID> | ||
</person_name> | ||
<person_name sequence="additional" | ||
contributor_role="author"> | ||
<given_name>Sarah E.</given_name> | ||
<surname>Bohndiek</surname> | ||
<ORCID>https://orcid.org/0000-0003-0371-8635</ORCID> | ||
</person_name> | ||
</contributors> | ||
<publication_date> | ||
<month>01</month> | ||
<day>19</day> | ||
<year>2024</year> | ||
</publication_date> | ||
<pages> | ||
<first_page>5686</first_page> | ||
</pages> | ||
<publisher_item> | ||
<identifier id_type="doi">10.21105/joss.05686</identifier> | ||
</publisher_item> | ||
<ai:program name="AccessIndicators"> | ||
<ai:license_ref applies_to="vor">http://creativecommons.org/licenses/by/4.0/</ai:license_ref> | ||
<ai:license_ref applies_to="am">http://creativecommons.org/licenses/by/4.0/</ai:license_ref> | ||
<ai:license_ref applies_to="tdm">http://creativecommons.org/licenses/by/4.0/</ai:license_ref> | ||
</ai:program> | ||
<rel:program> | ||
<rel:related_item> | ||
<rel:description>Software archive</rel:description> | ||
<rel:inter_work_relation relationship-type="references" identifier-type="doi">10.5281/zenodo.10255220</rel:inter_work_relation> | ||
</rel:related_item> | ||
<rel:related_item> | ||
<rel:description>GitHub review issue</rel:description> | ||
<rel:inter_work_relation relationship-type="hasReview" identifier-type="uri">https://github.com/openjournals/joss-reviews/issues/5686</rel:inter_work_relation> | ||
</rel:related_item> | ||
</rel:program> | ||
<doi_data> | ||
<doi>10.21105/joss.05686</doi> | ||
<resource>https://joss.theoj.org/papers/10.21105/joss.05686</resource> | ||
<collection property="text-mining"> | ||
<item> | ||
<resource mime_type="application/pdf">https://joss.theoj.org/papers/10.21105/joss.05686.pdf</resource> | ||
</item> | ||
</collection> | ||
</doi_data> | ||
<citation_list> | ||
<citation key="Beard2011"> | ||
<article_title>Biomedical photoacoustic | ||
imaging</article_title> | ||
<author>Beard</author> | ||
<journal_title>Interface Focus</journal_title> | ||
<issue>4</issue> | ||
<volume>1</volume> | ||
<doi>10.1098/rsfs.2011.0028</doi> | ||
<cYear>2011</cYear> | ||
<unstructured_citation>Beard, P. (2011). Biomedical | ||
photoacoustic imaging. Interface Focus, 1(4), 602–631. | ||
https://doi.org/10.1098/rsfs.2011.0028</unstructured_citation> | ||
</citation> | ||
<citation key="Brown2019"> | ||
<article_title>Photoacoustic imaging as a tool to probe the | ||
tumour microenvironment</article_title> | ||
<author>Brown</author> | ||
<journal_title>Disease Models & | ||
Mechanisms</journal_title> | ||
<issue>7</issue> | ||
<volume>12</volume> | ||
<doi>10.1242/dmm.039636</doi> | ||
<issn>1754-8403</issn> | ||
<cYear>2019</cYear> | ||
<unstructured_citation>Brown, E., Brunker, J., & | ||
Bohndiek, S. E. (2019). Photoacoustic imaging as a tool to probe the | ||
tumour microenvironment. Disease Models & Mechanisms, 12(7), | ||
dmm039636. https://doi.org/10.1242/dmm.039636</unstructured_citation> | ||
</citation> | ||
<citation key="Else2023"> | ||
<article_title>Dataset for: PATATO: A Python Photoacoustic | ||
Analysis Toolkit</article_title> | ||
<author>Else</author> | ||
<doi>10.17863/CAM.93181</doi> | ||
<cYear>2023</cYear> | ||
<unstructured_citation>Else, T., Groehl, J., Hacker, L., | ||
& Bohndiek, S. (2023). Dataset for: PATATO: A Python Photoacoustic | ||
Analysis Toolkit. | ||
https://doi.org/10.17863/CAM.93181</unstructured_citation> | ||
</citation> | ||
<citation key="Grohl2021"> | ||
<article_title>Learned spectral decoloring enables | ||
photoacoustic oximetry</article_title> | ||
<author>Gröhl</author> | ||
<journal_title>Scientific Reports</journal_title> | ||
<issue>1</issue> | ||
<volume>11</volume> | ||
<doi>10.1038/s41598-021-83405-8</doi> | ||
<cYear>2021</cYear> | ||
<unstructured_citation>Gröhl, J., Kirchner, T., Adler, T. | ||
J., Hacker, L., Holzwarth, N., Hernández-Aguilera, A., Herrera, M. A., | ||
Santos, E., Bohndiek, S. E., & Maier-Hein, L. (2021). Learned | ||
spectral decoloring enables photoacoustic oximetry. Scientific Reports, | ||
11(1), 6565. | ||
https://doi.org/10.1038/s41598-021-83405-8</unstructured_citation> | ||
</citation> | ||
<citation key="Grohl2022"> | ||
<article_title>SIMPA: An open-source toolkit for simulation | ||
and image processing for photonics and acoustics</article_title> | ||
<author>Gröhl</author> | ||
<journal_title>Journal of Biomedical Optics</journal_title> | ||
<issue>08</issue> | ||
<volume>27</volume> | ||
<doi>10.1117/1.JBO.27.8.083010</doi> | ||
<issn>1083-3668</issn> | ||
<cYear>2022</cYear> | ||
<unstructured_citation>Gröhl, J., Dreher, K. K., | ||
Schellenberg, M., Rix, T., Holzwarth, N., Vieten, P., Ayala, L., | ||
Bohndiek, S. E., Seitel, A., & Maier-Hein, L. (2022). SIMPA: An | ||
open-source toolkit for simulation and image processing for photonics | ||
and acoustics. Journal of Biomedical Optics, 27(08), 083010. | ||
https://doi.org/10.1117/1.JBO.27.8.083010</unstructured_citation> | ||
</citation> | ||
<citation key="Hochuli2019"> | ||
<article_title>Estimating blood oxygenation from | ||
photoacoustic images: Can a simple linear spectroscopic inversion ever | ||
work?</article_title> | ||
<author>Hochuli</author> | ||
<journal_title>Journal of Biomedical Optics</journal_title> | ||
<issue>12</issue> | ||
<volume>24</volume> | ||
<doi>10.1117/1.JBO.24.12.121914</doi> | ||
<issn>1083-3668</issn> | ||
<cYear>2019</cYear> | ||
<unstructured_citation>Hochuli, R., An, L., Beard, P. C., | ||
& Cox, B. T. (2019). Estimating blood oxygenation from photoacoustic | ||
images: Can a simple linear spectroscopic inversion ever work? Journal | ||
of Biomedical Optics, 24(12), 1. | ||
https://doi.org/10.1117/1.JBO.24.12.121914</unstructured_citation> | ||
</citation> | ||
<citation key="Kirchner2021"> | ||
<article_title>Multiple illumination learned spectral | ||
decoloring for quantitative optoacoustic oximetry | ||
imaging</article_title> | ||
<author>Kirchner</author> | ||
<journal_title>https://doi.org/10.1117/1.JBO.26.8.085001</journal_title> | ||
<issue>8</issue> | ||
<volume>26</volume> | ||
<doi>10.1117/1.JBO.26.8.085001</doi> | ||
<issn>1083-3668</issn> | ||
<cYear>2021</cYear> | ||
<unstructured_citation>Kirchner, T., & Frenz, M. (2021). | ||
Multiple illumination learned spectral decoloring for quantitative | ||
optoacoustic oximetry imaging. | ||
Https://Doi.org/10.1117/1.JBO.26.8.085001, 26(8), 085001. | ||
https://doi.org/10.1117/1.JBO.26.8.085001</unstructured_citation> | ||
</citation> | ||
<citation key="OKelly2021"> | ||
<article_title>A scalable open-source MATLAB toolbox for | ||
reconstruction and analysis of multispectral optoacoustic tomography | ||
data</article_title> | ||
<author>O’Kelly</author> | ||
<journal_title>Scientific Reports 2021 11:1</journal_title> | ||
<issue>1</issue> | ||
<volume>11</volume> | ||
<doi>10.1038/s41598-021-97726-1</doi> | ||
<issn>2045-2322</issn> | ||
<isbn>0123456789</isbn> | ||
<cYear>2021</cYear> | ||
<unstructured_citation>O’Kelly, D., Campbell, J., Gerberich, | ||
J. L., Karbasi, P., Malladi, V., Jamieson, A., Wang, L., & Mason, R. | ||
P. (2021). A scalable open-source MATLAB toolbox for reconstruction and | ||
analysis of multispectral optoacoustic tomography data. Scientific | ||
Reports 2021 11:1, 11(1), 1–18. | ||
https://doi.org/10.1038/s41598-021-97726-1</unstructured_citation> | ||
</citation> | ||
<citation key="Prahl2018"> | ||
<article_title>Assorted Spectra</article_title> | ||
<author>Prahl</author> | ||
<cYear>2018</cYear> | ||
<unstructured_citation>Prahl, S. (2018). Assorted Spectra. | ||
https://omlc.org/spectra/index.html.</unstructured_citation> | ||
</citation> | ||
<citation key="Regensburger2021"> | ||
<article_title>Optoacoustic Imaging in | ||
Inflammation</article_title> | ||
<author>Regensburger</author> | ||
<journal_title>Biomedicines</journal_title> | ||
<issue>5</issue> | ||
<volume>9</volume> | ||
<doi>10.3390/biomedicines9050483</doi> | ||
<issn>2227-9059</issn> | ||
<cYear>2021</cYear> | ||
<unstructured_citation>Regensburger, A. P., Brown, E., | ||
Krönke, G., Waldner, M. J., & Knieling, F. (2021). Optoacoustic | ||
Imaging in Inflammation. Biomedicines, 9(5), 483. | ||
https://doi.org/10.3390/biomedicines9050483</unstructured_citation> | ||
</citation> | ||
<citation key="Shen2020"> | ||
<article_title>Negativity artifacts in back-projection based | ||
photoacoustic tomography</article_title> | ||
<author>Shen</author> | ||
<journal_title>Journal of Physics D: Applied | ||
Physics</journal_title> | ||
<issue>7</issue> | ||
<volume>54</volume> | ||
<doi>10.1088/1361-6463/ABC37D</doi> | ||
<issn>0022-3727</issn> | ||
<cYear>2020</cYear> | ||
<unstructured_citation>Shen, K., Liu, S., Feng, T., Yuan, | ||
J., Zhu, B., & Tian, C. (2020). Negativity artifacts in | ||
back-projection based photoacoustic tomography. Journal of Physics D: | ||
Applied Physics, 54(7), 074001. | ||
https://doi.org/10.1088/1361-6463/ABC37D</unstructured_citation> | ||
</citation> | ||
<citation key="Steinberg2019"> | ||
<article_title>Photoacoustic clinical | ||
imaging</article_title> | ||
<author>Steinberg</author> | ||
<journal_title>Photoacoustics</journal_title> | ||
<volume>14</volume> | ||
<doi>10.1016/j.pacs.2019.05.001</doi> | ||
<cYear>2019</cYear> | ||
<unstructured_citation>Steinberg, I., Huland, D. M., | ||
Vermesh, O., Frostig, H. E., Tummers, W. S., & Gambhir, S. S. | ||
(2019). Photoacoustic clinical imaging. Photoacoustics, 14, 77–98. | ||
https://doi.org/10.1016/j.pacs.2019.05.001</unstructured_citation> | ||
</citation> | ||
<citation key="Tomaszewski2018"> | ||
<article_title>Oxygen-enhanced and dynamic contrast-enhanced | ||
optoacoustic tomography provide surrogate biomarkers of tumour vascular | ||
function, hypoxia and necrosis.</article_title> | ||
<author>Tomaszewski</author> | ||
<journal_title>Cancer Research</journal_title> | ||
<issue>20</issue> | ||
<volume>78</volume> | ||
<doi>10.1158/0008-5472.CAN-18-1033</doi> | ||
<issn>0008-5472</issn> | ||
<cYear>2018</cYear> | ||
<unstructured_citation>Tomaszewski, M. R., Gehrung, M., | ||
Joseph, J., Quiros Gonzalez, I., Disselhorst, J. A., & Bohndiek, S. | ||
E. (2018). Oxygen-enhanced and dynamic contrast-enhanced optoacoustic | ||
tomography provide surrogate biomarkers of tumour vascular function, | ||
hypoxia and necrosis. Cancer Research, 78(20), canres.1033.2018. | ||
https://doi.org/10.1158/0008-5472.CAN-18-1033</unstructured_citation> | ||
</citation> | ||
<citation key="Wang2012"> | ||
<article_title>Photoacoustic Tomography: In Vivo Imaging | ||
from Organelles to Organs</article_title> | ||
<author>Wang</author> | ||
<journal_title>Science</journal_title> | ||
<issue>6075</issue> | ||
<volume>335</volume> | ||
<doi>10.1126/science.1216210</doi> | ||
<issn>0036-8075</issn> | ||
<cYear>2012</cYear> | ||
<unstructured_citation>Wang, L. V., & Hu, S. (2012). | ||
Photoacoustic Tomography: In Vivo Imaging from Organelles to Organs. | ||
Science, 335(6075), 1458–1462. | ||
https://doi.org/10.1126/science.1216210</unstructured_citation> | ||
</citation> | ||
<citation key="Xu2005"> | ||
<article_title>Universal back-projection algorithm for | ||
photoacoustic computed tomography</article_title> | ||
<author>Xu</author> | ||
<journal_title>Physical Review E - Statistical, Nonlinear, | ||
and Soft Matter Physics</journal_title> | ||
<issue>1</issue> | ||
<volume>71</volume> | ||
<doi>10.1103/PhysRevE.71.016706</doi> | ||
<cYear>2005</cYear> | ||
<unstructured_citation>Xu, M., & Wang, L. V. (2005). | ||
Universal back-projection algorithm for photoacoustic computed | ||
tomography. Physical Review E - Statistical, Nonlinear, and Soft Matter | ||
Physics, 71(1). | ||
https://doi.org/10.1103/PhysRevE.71.016706</unstructured_citation> | ||
</citation> | ||
</citation_list> | ||
</journal_article> | ||
</journal> | ||
</body> | ||
</doi_batch> |
Oops, something went wrong.