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TGFβ-mediated dural progenitor cell migration into the coronal suture is crucial for preventing craniosynostosis.

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Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

Jupyter notebook · 86 lines · 1.7 KB · CC-BY-4.0

  1. # %%
  2. import nibabel as nib
  3. import numpy as np
  6. # %%
  8. # 1. 读入annotation文件
  9. annotation_file = "E:/Suture/01_mouse skull CT_develop/Brain_MRI_annotation/E11.5/E11-5_DevCCF_Annotations_31.5um.nii.gz"
  14. # %%
  15. img = nib.load(annotation_file)
  16. data = img.get_fdata()
  18. # %%
  20. # 2. 计算体素体积（单位：mm³）
  21. voxel_size_um = 31.5
  22. voxel_volume_mm3 = (voxel_size_um / 1000) ** 3
  26. # %%
  27. # 3. 统计每个标签ID的体素数和体积
  28. labels = np.unique(data)
  29. for label in labels:
  30. if label == 0: # 跳过背景
  31. continue
  32. voxel_count = np.sum(data == label)
  33. volume = voxel_count * voxel_volume_mm3
  34. print(f"Label {int(label)}: {voxel_count} voxels, Volume = {volume:.4f} mm³")
  36. # %%
  37. import nibabel as nib
  38. import numpy as np
  39. import pandas as pd
  43. # %%
  44. # 1. 读入annotation文件
  45. annotation_file = "E:/Suture/01_mouse skull CT_develop/Brain_MRI_annotation/P56/P56_DevCCF_Annotations_20um.nii.gz"
  46. img = nib.load(annotation_file)
  47. data = img.get_fdata()
  51. # %%
  52. # 2. 计算体素体积（单位：mm³）
  53. voxel_size_um = 20
  54. voxel_volume_mm3 = (voxel_size_um / 1000) ** 3
  57. # %%
  58. # 3. 统计每个标签ID的体素数和体积
  59. labels = np.unique(data)
  60. results = []
  62. for label in labels:
  63. if label == 0: # 跳过背景
  64. continue
  65. voxel_count = np.sum(data == label)
  66. volume = voxel_count * voxel_volume_mm3
  67. results.append({
  68. 'Label ID': int(label),
  69. 'Voxel Count': voxel_count,
  70. 'Volume (mm³)': volume
  71. })
  73. # %%
  74. # 4. 生成DataFrame
  75. df = pd.DataFrame(results)
  77. # %%
  78. # 5. 导出为Excel
  79. output_file = "E:/Suture/01_mouse skull CT_develop/Brain_MRI_annotation/P56/P56_brain_volumes_20um.xlsx"
  81. # %%
  82. df.to_excel(output_file, index=False)
  83. print(f"导出完成，文件保存到：{output_file}")
  85. # %%

brain volume.ipynb, under CC-BY-4.0 · at the source

Overview

Authors: Peng Chen1, Lin Meng1, Lin Lan1, Jifan Feng1, Tingwei Guo1, Lu Gao1, Hana Hekmat1, Calista Ly1, Mingyi Zhang1, Sa Cha1, Thach-Vu Ho1, Yang Chai1
ORCID iDs: Lin Meng, Sa Cha, Yang Chai
  1. Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California,Los Angeles, CA USA
Institutions: University of Southern California (United States)
Journal: Nature communications, volume 17, issue 1, article 6601
Dates: received 15 August 2025; accepted 7 May 2026; published online 19 May 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s41467-026-73292-w · PMID 42156771 · PMCID PMC13381870 · OpenAlex W7161635905
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), mouse (organism)
Methods: Statistics, Smoothing, state filtering, decompositions
Keywords: Growth factor signalling, Disease model, Mesenchymal migration
MeSH: Cell Movement*, Cranial Sutures*, Craniosynostoses*, Dura Mater*, Stem Cells*, Transforming Growth Factor beta*, Acrocephalosyndactylia, Animals, Humans, Mesoderm, Mice, Mice, Knockout, Neural Crest, Nuclear Proteins, Receptor, Transforming Growth Factor-beta Type II, Signal Transduction, Twist-Related Protein 1, Zinc Finger Protein GLI1 (* major topic)
Topic: Craniofacial Disorders and Treatments (Genetics, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR) (R01DE0030901)
Citations: not cited yet (Europe PMC); 64 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above.

Zenodo 19664792

License: CC-BY-4.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Languages: Jupyter (1)
Size: 1 file, 1 script
Software Heritage: not checked
Found in: “Code availability”
Holds: 1 notebook
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NiBabel (1 file), NumPy (1 file), pandas (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
1 file
At the source:

Code availability statement

The paper has a code availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

  • it points to the authors' code: Zenodo 19664792

Read it in the paper: doi.org/10.1038/s41467-026-73292-w.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 1 script, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

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

Data availability statement

The paper has a data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

  • no repository, dataset or request procedure was recognized in it

Read it in the paper: doi.org/10.1038/s41467-026-73292-w.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 12 authors, 3 keywords, 18 MeSH terms, 1 funder, 63 references.

Cite

This paper

Chen, P., Meng, L., Lan, L., Feng, J., Guo, T., Gao, L., Hekmat, H., Ly, C., Zhang, M., Cha, S., Ho, T.-V., & Chai, Y. (2026). TGFβ-mediated dural progenitor cell migration into the coronal suture is crucial for preventing craniosynostosis. Nature communications, 17(1), 6601. https://doi.org/10.1038/s41467-026-73292-w

BibTeX

@article{chen2026tgf,
author = {Chen, Peng and Meng, Lin and Lan, Lin and Feng, Jifan and Guo, Tingwei and Gao, Lu and Hekmat, Hana and Ly, Calista and Zhang, Mingyi and Cha, Sa and Ho, Thach-Vu and Chai, Yang},
title = {{TGFβ-mediated dural progenitor cell migration into the coronal suture is crucial for preventing craniosynostosis}},
journal = {Nature communications},
year = {2026},
month = may,
volume = {17},
number = {1},
pages = {6601},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-026-73292-w},
url = {https://doi.org/10.1038/s41467-026-73292-w},
pmid = {42156771},
pmcid = {PMC13381870}
}

RIS

TY - JOUR
AU - Chen, Peng
AU - Meng, Lin
AU - Lan, Lin
AU - Feng, Jifan
AU - Guo, Tingwei
AU - Gao, Lu
AU - Hekmat, Hana
AU - Ly, Calista
AU - Zhang, Mingyi
AU - Cha, Sa
AU - Ho, Thach-Vu
AU - Chai, Yang
TI - TGFβ-mediated dural progenitor cell migration into the coronal suture is crucial for preventing craniosynostosis
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/05/19
VL - 17
IS - 1
SP - 6601
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/s41467-026-73292-w
UR - https://doi.org/10.1038/s41467-026-73292-w
LA - en
ER -

CSL-JSON

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"id": "10.1038/s41467-026-73292-w",
"type": "article-journal",
"title": "TGFβ-mediated dural progenitor cell migration into the coronal suture is crucial for preventing craniosynostosis",
"container-title": "Nature communications",
"author": [
{
"family": "Chen",
"given": "Peng"
},
{
"family": "Meng",
"given": "Lin"
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{
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"given": "Lin"
},
{
"family": "Feng",
"given": "Jifan"
},
{
"family": "Guo",
"given": "Tingwei"
},
{
"family": "Gao",
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},
{
"family": "Hekmat",
"given": "Hana"
},
{
"family": "Ly",
"given": "Calista"
},
{
"family": "Zhang",
"given": "Mingyi"
},
{
"family": "Cha",
"given": "Sa"
},
{
"family": "Ho",
"given": "Thach-Vu"
},
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"family": "Chai",
"given": "Yang"
}
],
"container-title-short": "Nat Commun",
"volume": "17",
"issue": "1",
"page": "6601",
"DOI": "10.1038/s41467-026-73292-w",
"PMID": "42156771",
"PMCID": "PMC13381870",
"ISSN": "2041-1723",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s41467-026-73292-w",
"language": "en",
"issued": {
"date-parts": [
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5,
19
]
]
}
}

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