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Measuring cerebral glucose metabolism by chemical exchange-sensitive spin-lock (CESL) MRI of 2-deoxy-D-glucose in rodents.

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  1. Readme
  2. Open Data Repository
  4. ******************************************************************************************************************
  5. Manuscript information
  6. ******************************************************************************************************************
  7. 2-Deoxy-D-Glucose chemical exchange-sensitive spin-lock MRI of cerebral metabolism after stroke in the rat
  9. Authors: Philipp Boehm-Sturm, Patrick Schuenke, Marco Foddis, Susanne Mueller, Stefan P. Koch, Daniel J. Beard,
  10. Paul Holloway, Amin Mottahedin, Leif Schröder, Alastair M. Buchan, Philipp Mergenthaler
  12. Preprint: LINK TO BIORXIV HERE
  14. Last updated: 2024/12/18
  16. ******************************************************************************************************************
  17. Contact
  18. ******************************************************************************************************************
  20. PD Dr. Philipp Mergenthaler
  21. Charité-Universitätsmedizin Berlin,
  22. Department of Neurology with Experimental Neurology and Center for Stroke Research
  23. Charitéplatz 1, 10117 Berlin, Germany
  24. email: [email hidden]
  26. Prof. Dr. Philipp Boehm-Sturm
  27. Charité-Universitätsmedizin Berlin,
  28. Charité 3R - Replace|Reduce|Refine, Department of Experimental Neurology and Center for Stroke Research
  29. Charitéplatz 1, 10117 Berlin, Germany
  30. email: [email hidden]
  32. ******************************************************************************************************************
  33. Description
  34. ******************************************************************************************************************
  35. This dataset contains in vivo MRI data of rats after 90 min proximal MCAO
  37. ******************************************************************************************************************
  38. Folder and subfolder names
  39. ******************************************************************************************************************
  41. dat - directory containing processed datasets including ANTx2 (https://github.com/ChariteExpMri/antx2) project file
  42. - All subdirectories (MRI IDs) follow the follwing name structure:
  43. [ExperimentDate]_[InitialsExperimenter]_[GroupNumber]_[SubjectNumber] e.g. 20200716SA_G1_D7
  45. raw - directory containing Bruker raw data, documentation of individual scans in documentation_scan_numbers_rawData.xlsx
  47. code - directory containing scripts for processing the data with ANTx2/MATLAB
  49. results - directory containing statistic results
  51. templates - directory containing the SIGMA rat brain template and atlas used for processing
  54. ******************************************************************************************************************
  55. List of files
  56. ******************************************************************************************************************
  58. README.txt - (this file)
  59. documentation_scan_numbers_rawData.xlsx - assignment of scan numbers
  61. dat directory also contains many intermediate files, only important ones are documented here:
  63. t2.nii / x_t2.nii t2 weighted MRI in the native (raw data) / atlas space
  65. 07_DWI_Trace_EPI_sat_XX_1.nii diffusion MRI raw data
  67. 08_Perfusion_FAIR_EPI_studyShim_XX_1.nii Perfusion MRI raw data
  71. T1rho_2DG__001.nii CESL MRI raw data containing 13 spin lock frames
  73. c_c_T1rho_2DG__001.nii Motion corrected CESL MRI raw data, i.e. registered to the first CESL scan, used for calculating R1rho maps
  75. c_CBF_CBFcorrected_slice.nii Calculated CBF map in registration with R1rho maps
  76. c_ADC_ADC_slice.nii Calculated ADC map in registration with R1rho maps
  78. mean_R1rho_001-005.nii baseline R1rho map used for calculating deltaR1rho
  79. mean_R1rho_031-035.nii late R1rho map used for segmenting the metabolic lesion and for quantitative analyses
  81. deltaR1rho_i.nii; i=001-035 calculated delta R1rho maps, coregistered to the first T1rho images
  83. mask_Core__fromADC.nii mask of lesion core from ADC, registered to R1rho maps
  84. mask_Core__fromADC_mirror.nii mask of lesion core from ADC, registered to R1rho maps and mirrored at midline in atlas space, then backtransformed
  86. mask_Hypoperfused__fromCBF.nii mask of hypoperfused area from CBF, registered to R1rho maps
  87. mask_Hypoperfused__fromCBF_mirror.nii mask of hypoperfused area from CBF, registered to R1rho maps, registered to R1rho maps and mirrored at midline in atlas space, then backtransformed
  89. mask_Penumbra.nii mask of penumbra (mismatch of the above)
  90. mask_Penumbra_mirror.nii mask of penumbra (mismatch of the above), mirrored at midline in atlas space, then backtransformed

README.txt, under CC-BY-4.0 · at the source

Overview

Authors: Philipp Boehm-Sturm1,2,3, Patrick Schuenke4,5, Marco Foddis1,2,3, Susanne Mueller1,2,3, Stefan P Koch1,2,3, Daniel J Beard6, Paul Holloway7,8, Amin Mottahedin7,8,9, Leif Schröder10,11,12, Alastair M Buchan1,7,8, Philipp Mergenthaler1,3,7,8
ORCID iDs: Philipp Boehm-Sturm, Patrick Schuenke, Stefan P Koch, Amin Mottahedin, Philipp Mergenthaler
  1. Charité-Universitätsmedizin Berlin, Center for Stroke Research Berlin, Berlin, Germany
  2. Charité-Universitätsmedizin Berlin, Experimental Imaging at the Charité for 3R (EPIC3R), Charité 3R – Replace | Reduce | Refine, Berlin, Germany
  3. Charité-Universitätsmedizin Berlin, Department of Neurology with Experimental Neurology, Berlin, Germany
  4. Charité-Universitätsmedizin Berlin, Department of Radiology, Berlin, Germany
  5. Physikalisch-Technische Bundesanstalt (PTB), Braunschweig and Berlin, Germany
  6. The University of Newcastle, School of Biomedical Sciences and Pharmacy, Newcastle, Australia
  7. Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
  8. Consortium International pour la Recherche Circadienne sur l’AVC (CIRCA)
  9. Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
  10. German Cancer Research Center, Translational Molecular Imaging, Heidelberg, Germany
  11. Department for Physics and Astronomy, Ruprecht Karls University Heidelberg, Heidelberg, Germany
  12. German Cancer Consortium (DKTK), Heidelberg, Germany
Institutions: Center for Stroke Research Berlin (Germany); Charité – Universitätsmedizin Berlin (Germany); Physikalisch-Technische Bundesanstalt (Germany); University of Newcastle Australia (Australia); University of Oxford (United Kingdom); German Cancer Research Center (Germany); Heidelberg University (Germany); Deutsches Konsortium für Translationale Krebsforschung (Germany)
Journal: PloS one, volume 21, issue 3, article e0346046
Dates: received 1 August 2025; accepted 14 March 2026; published online 27 March 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1371/journal.pone.0346046 · PMID 41894465 · PMCID PMC13028544 · OpenAlex W7141402767
Open access: gold, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Categories: structural MRI / diffusion (modality), human (organism), rat (organism), stroke (population)
MeSH: Brain*, Deoxyglucose*, Glucose*, Magnetic Resonance Imaging*, Animals, Male, Rats, Rats, Sprague-Dawley, Stroke (* major topic)
Topic: Lanthanide and Transition Metal Complexes (Materials Chemistry, Materials Science), according to OpenAlex
Funding: Deutsche Forschungsgemeinschaft (EXC-2049 – 390688,087, BO4484/2‐1, 424778381); Fondation Leducq (21CVD04); Bundesministerium für Bildung und Forschung (01EW2305); Einstein Stiftung Berlin (EVF2021619, EJF-2020-602, EVF-2021-619-2)
Citations: not cited yet (Europe PMC); 14 references in the paper

Abstract

Magnetic resonance imaging (MRI) of glucose metabolism shows significant potential for identifying disease biomarkers and monitoring therapeutic responses in neurological conditions. Here, we present a protocol utilizing chemical exchange-sensitive spin-lock (CESL) MRI with the glucose analogue 2-deoxy-D-glucose (2DG) in the rat brain. We employed this method to characterize metabolic changes in ischemic tissue in a rat model of stroke. However, the utility of the technique is not limited to stroke and may be adapted to other disease models with minimal modifications. Previous research has demonstrated that CESL MRI is sensitive to various glucose analogs, including regular D-glucose, which is suitable for human application. Consequently, our protocol provides a foundation for a wide range of future applications in both basic and translational research, with potential utility in animal models and, eventually, human studies.

Reproduced under the paper's license (CC BY), from the paper cited above.

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Zenodo 14526092

License: CC-BY-4.0
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Size: 3 files
Software Heritage: not checked
Found in: “Data Availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 30 September 2026: the link answers (HTTP 200)
  • 30 September 2026: the link answers (HTTP 200)
1 file
At the source: zenodo.org/records/14526092

Zenodo 14526091

License: CC-BY-4.0
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Size: 3 files
Software Heritage: not checked
Found in: “Data Availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 30 September 2026: the link answers (HTTP 200)
  • 30 September 2026: the link answers (HTTP 200)
1 file
At the source: doi.org/10.5281/zenodo.14526091

The paper's code and data availability statement is in the Data section.

Tracing map

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  • 0 scripts, each with its path and the digest of its content;
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Data

No dataset and no data link were found in the paper.

Data Availability

Data and code associated with this manuscript are available on Zenodo (https://zenodo.org/records/14526092; DOI: 10.5281/zenodo.14526091 (https://doi.org/10.5281/zenodo.14526091)), including MRI image data to reproduce the steps described in this protocol.

Reproduced under the paper's license (CC BY), from the paper cited above.

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Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 11 authors, 9 MeSH terms, 4 funders, 14 references.

Cite

This paper

Boehm-Sturm, P., Schuenke, P., Foddis, M., Mueller, S., Koch, S. P., Beard, D. J., Holloway, P., Mottahedin, A., Schröder, L., Buchan, A. M., & Mergenthaler, P. (2026). Measuring cerebral glucose metabolism by chemical exchange-sensitive spin-lock (CESL) MRI of 2-deoxy-D-glucose in rodents. PloS one, 21(3), e0346046. https://doi.org/10.1371/journal.pone.0346046

BibTeX

@article{boehmsturm2026measuring,
author = {Boehm-Sturm, Philipp and Schuenke, Patrick and Foddis, Marco and Mueller, Susanne and Koch, Stefan P and Beard, Daniel J and Holloway, Paul and Mottahedin, Amin and Schröder, Leif and Buchan, Alastair M and Mergenthaler, Philipp},
title = {{Measuring cerebral glucose metabolism by chemical exchange-sensitive spin-lock (CESL) MRI of 2-deoxy-D-glucose in rodents}},
journal = {PloS one},
year = {2026},
month = mar,
volume = {21},
number = {3},
pages = {e0346046},
publisher = {PLOS},
issn = {1932-6203},
doi = {10.1371/journal.pone.0346046},
url = {https://doi.org/10.1371/journal.pone.0346046},
pmid = {41894465},
pmcid = {PMC13028544}
}

RIS

TY - JOUR
AU - Boehm-Sturm, Philipp
AU - Schuenke, Patrick
AU - Foddis, Marco
AU - Mueller, Susanne
AU - Koch, Stefan P
AU - Beard, Daniel J
AU - Holloway, Paul
AU - Mottahedin, Amin
AU - Schröder, Leif
AU - Buchan, Alastair M
AU - Mergenthaler, Philipp
TI - Measuring cerebral glucose metabolism by chemical exchange-sensitive spin-lock (CESL) MRI of 2-deoxy-D-glucose in rodents
T2 - PloS one
J2 - PLoS One
PY - 2026
DA - 2026/03/27
VL - 21
IS - 3
SP - e0346046
SN - 1932-6203
PB - PLOS
DO - 10.1371/journal.pone.0346046
UR - https://doi.org/10.1371/journal.pone.0346046
LA - en
ER -

CSL-JSON

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