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MicroFace maps microglial morphology remodeling, revealing spatial zones and bifurcated trajectories during brain microinjury recovery.

Code ↔ Paper

7 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 7 matches
  1. [1] § STAR★Methods › Quantification and statistical analysis › Morphometric analysis › Outlier detection ↔ Data analysis/Scripts/03_Wins_Filtering_PCA.R, lines 43–83 · score 0.75 · chi squared distribution, Mahalanobis distance, cutoff, winsorized, outliers, detection
  2. [2] § Results › Rod-like and reactive transitional microglia represent distinct intermediate states during injury response ↔ Imaging data analysis/Scripts/02_Functions.R, lines 44–92 · score 0.66 · major axis length, Feret diameter, trunk branches, soma, injury, cells
  3. [3] § Results › Validation of the MicroFace segmentation and morphometric quantification pipeline ↔ Data analysis/Scripts/Figure_2.R, lines 90–133 · score 0.66 · convex area, Feret diameter, MicroFace, solidity, radius, Correlation
  4. [4] § Results › Coordinated morphometric programs reveal spatially organized microglial remodeling after implantation ↔ Data analysis/Scripts/Figure_3.R, lines 1–40 · score 0.63 · morphometric features, coefficient, morphological features, microglial morphology, rank, NMF
  5. [5] § Results › Rod-like and reactive transitional microglia represent distinct intermediate states during injury response ↔ Data analysis/Scripts/02_Import_Data.R, lines 142–180 · score 0.61 · major axis length, Feret diameter, perimeter, rod, soma, morphological
  6. [6] § Results › Validation of the MicroFace segmentation and morphometric quantification pipeline ↔ Data analysis/Scripts/Figure_2.R, lines 45–88 · score 0.55 · Cell perimeter, Cell area, MicroFace, Scatterplots, Correlation, Figure 2
  7. [7] § Results › Coordinated morphometric programs reveal spatially organized microglial remodeling after implantation ↔ Imaging data analysis/Scripts/02_Functions.R, lines 1–42 · score 0.53 · morphological parameters, ramification, microglial morphology, ratio, perimeter, soma

Paper

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The authors' code

R · 92 lines · 2.9 KB · no license · 2 matches

  1. # ===================================================
  2. # MICROGLIA MORPHOLOGICAL ANALYSIS PIPELINE
  3. # ===================================================
  5. # -------------------------------
  6. # 1. DISTANCE CALCULATIONS & BINNING
  7. # -------------------------------
  9. # Calculate radial distance from injury center (2764, 2196)
  10. import$df_all <- import$df_all %>%
  11. mutate(
  12. radial_dist = sqrt((Center_X_soma - Injury_x)^2 + (Center_Y_soma - Injury_y)^2),
  14. # Create 25 bins based on distance
  15. bin_number = ntile(radial_dist, 25),
  16. bin_range = bin_number * 139,
  18. # Consolidate bins >16 into single bin (17)
  19. Bin_Number_New = ifelse(bin_number > 16, 17, bin_number),
  20. bin_range_new = Bin_Number_New * 139,
  22. # Classify impact regions
  23. Impact_Region = case_when(
  24. Bin_Number_New <= 5 ~ "Near",
  25. Bin_Number_New >= 8 ~ "Far",
  26. TRUE ~ "Middle"
  27. )
  28. )
  30. # -------------------------------
  31. # 2. MORPHOLOGICAL METRICS CALCULATION
  32. # -------------------------------
  34. # Calculate various morphological parameters
  35. import$df_all <- import$df_all %>%
  36. mutate(
  37. # Ramification Index
  38. RI = (Perimeter_cell / Area_cell) / (2 * sqrt(pi / Area_cell)),
  40. # Area ratios
  41. area_ratio = Area_cell / Area_soma,
  42. Cyto_Area = Area_cell - Area_soma,
  44. # Length/Width ratios
  45. Length_Width_Ratio_cell = MaxFeretDiameter_cell / MinFeretDiameter_cell,
  46. Length_Width_Ratio_soma = MaxFeretDiameter_soma / MinFeretDiameter_soma,
  48. # Aspect ratios
  49. Aspect_Ratio_cell = MajorAxisLength_cell / MinorAxisLength_cell,
  50. Aspect_Ratio_soma = MajorAxisLength_soma / MinorAxisLength_soma,
  52. # Branching metrics
  53. Branch_Ratio = Non_Trunk_Branch / Trunk_Branch,
  54. Total_Branch = Non_Trunk_Branch + Trunk_Branch,
  56. # Health score (0-1 scale)
  57. Health_score = case_when(
  58. Total_Branch >= 20 ~ 1,
  59. TRUE ~ (1 - ((20 - Total_Branch) / 2)/10)
  60. )
  61. )
  63. # -------------------------------
  64. # 3. COLOR PALETTES
  65. # -------------------------------
  66. company_colors <- c("#E50000", "#008A8A", "#AF0076", "#E56800", "#1717A0", "#E5AC00", "#00B700")
  67. company_colors2 <- c("#E50000", "#0080FF","#E56800", "#AF0076", "#1717A0")
  68. morpho_colours <- c("#FF0000", "#00FF00", "#0000FF", "#FFFF00", "#FF00FF", "#00FFFF",
  69. "#FF8000", "#8000FF", "#00FF80", "#FF0080", "#0080FF", "#80FF00",
  70. "#800000", "#008000")
  73. # -------------------------------
  74. # 4. DATA REORGANIZATION
  75. # -------------------------------
  77. # Reorder columns to prioritize important variables
  78. import$df_all_reordered <- import$df_all %>%
  79. dplyr::select(
  80. # Selected important columns first
  81. c(9:14,19,29,32,33,34,37,38,39,40,41,42,47,57,60,65:72),
  82. # All remaining columns
  83. everything()
  84. )
  87. # -------------------------------
  88. # 5. DATA EXPORT
  89. # -------------------------------
  90. write.csv(import$df_all_reordered,
  91. "D:/Brain Injury project/4 Datasheet/df_all_reordered.csv",
  92. row.names = FALSE)

02_Functions.R at commit 9e04611, no license · at the source

Overview

Authors: Vatsal D. Jariwala1,2,3, Shreya Ponnamma1,2, Vidhya M. Ravi2,3,4,5, Jürgen Beck3,4, Ulrich G. Hofmann3,4,6, Kevin Joseph1,3,4
ORCID iDs: Vatsal D. Jariwala, Kevin Joseph
  1. Laboratory for NeuroEngineering, Department of Neurosurgery, Medical Center-University of Freiburg, Freiburg, Germany
  2. 3D Brain Models Lab, Department of Neurosurgery, Medical Center-University of Freiburg, Freiburg, Germany
  3. Department of Neurosurgery, Medical Center-University of Freiburg, Freiburg, Germany
  4. Faculty of Medicine, University of Freiburg, Freiburg, Germany
  5. Freiburg Institute for Advanced Science (FRIAS), University of Freiburg, Freiburg, Germany
  6. Neuroelectronic Systems, Department of Neurosurgery, Medical Center-University of Freiburg, Freiburg, Germany
Institutions: University of Freiburg (Germany); University Medical Center Freiburg (Germany)
Journal: iScience, volume 29, issue 7, article 116485
Dates: received 18 July 2025; accepted 4 June 2026; published online 23 June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1016/j.isci.2026.116485 · PMID 42389604 · PMCID PMC13320269 · OpenAlex W7165613008
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Machine learning, Connectivity
Keywords: health sciences, biological sciences, cellular physiology, cell biology, functional aspects of cell biology
Topic: Neuroinflammation and Neurodegeneration Mechanisms (Neurology, Neuroscience), according to OpenAlex
Funding: German Research Foundation
Citations: not cited yet (Europe PMC); 60 references in the paper
Research resources: GFAP RRID:AB_10013382, Iba1 RRID:AB_839504

Abstract

Microglia undergo morphological remodeling in response to brain injury, yet large-scale quantification of these changes remains limited. Here, we present MicroFace, an automated image analysis pipeline for high-throughput reconstruction and morphometric profiling of microglia from immunofluorescence images. We applied MicroFace to 279,510 microglia from the rodent cortex following localized microinjury induced by neural probe implantation. Spatiotemporal analysis revealed distinct morphotypes spanning ramified and amoeboid states, organized along spatial gradients relative to the injury site and evolving over time. We identify a bifurcated response characterized by divergent intermediate morphologies, including reactive transient cells and elongated rod-like microglia enriched near the injury. Integration with transcriptomic datasets suggests that rod-like microglia represent a morphologically and transcriptionally distinct subset associated with immunomodulatory functions. These findings define dynamic and heterogeneous microglial adaptations to brain injury and highlight morphology as a key indicator of functional state.

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

Repositories

Its files are read in the Code ↔ Paper reader above, with 7 matches between paragraphs and lines of code.

Vatsjari/MicroFace

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 899bcea357f9d0360f5138fb7038c37e6c06f7c9, 11 May 2026
Languages: R (12)
Size: 33 files, 12 scripts
Software Heritage: not checked
Found in: “Data and code availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: tidyverse (6 files), ggplot2 (2 files), reshape2 (2 files), patchwork (1 file), reticulate (1 file), UMAP (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
13 files
At the source: github.com/Vatsjari/MicroFace

3DBMandNE-Lab/MicroFace

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 9e04611e5936f69f4d8c8079885a2a9547880617, 6 July 2025
Languages: R (7)
Size: 76 files, 7 scripts
Software Heritage: not archived
Found in: “Data and code availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: tidyverse (4 files), ggpubr (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
8 files
At the source: github.com/3DBMandNE-Lab/MicroFace

Zenodo 20325902

License: CC-BY-4.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: the references
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
At the source:

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

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:

  • 3 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 19 scripts, each with its path and the digest of its content;
  • 7 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • 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 and code availability

• Processed morphometric datasets generated in this study are available at Zenodo.51 A subset of raw immunofluorescence images and corresponding segmentation masks generated using the MicroFace toolbox are also available at Zenodo.51 Publicly available transcriptomic datasets analyzed in this study are available from Gene Expression Omnibus (GEO) under accession numbers GSE226211 and GSE226208. • All scripts and the MicroFace toolbox used in this study are publicly available through GitHub: https://github.com/Vatsjari/MicroFace; https://github.com/3DBMandNE-Lab/MicroFace. • Any additional information required is available from the lead contact upon request.

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

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, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 5 keywords, 1 funder, 60 references, 2 RRIDs.

Cite

This paper

Jariwala, V. D., Ponnamma, S., Ravi, V. M., Beck, J., Hofmann, U. G., & Joseph, K. (2026). MicroFace maps microglial morphology remodeling, revealing spatial zones and bifurcated trajectories during brain microinjury recovery. iScience, 29(7), 116485. https://doi.org/10.1016/j.isci.2026.116485

BibTeX

@article{jariwala2026microface,
author = {Jariwala, Vatsal D. and Ponnamma, Shreya and Ravi, Vidhya M. and Beck, Jürgen and Hofmann, Ulrich G. and Joseph, Kevin},
title = {{MicroFace maps microglial morphology remodeling, revealing spatial zones and bifurcated trajectories during brain microinjury recovery}},
journal = {iScience},
year = {2026},
month = jun,
volume = {29},
number = {7},
pages = {116485},
publisher = {Elsevier},
issn = {2589-0042},
doi = {10.1016/j.isci.2026.116485},
url = {https://doi.org/10.1016/j.isci.2026.116485},
pmid = {42389604},
pmcid = {PMC13320269}
}

RIS

TY - JOUR
AU - Jariwala, Vatsal D.
AU - Ponnamma, Shreya
AU - Ravi, Vidhya M.
AU - Beck, Jürgen
AU - Hofmann, Ulrich G.
AU - Joseph, Kevin
TI - MicroFace maps microglial morphology remodeling, revealing spatial zones and bifurcated trajectories during brain microinjury recovery
T2 - iScience
J2 - iScience
PY - 2026
DA - 2026/06/23
VL - 29
IS - 7
SP - 116485
SN - 2589-0042
PB - Elsevier
DO - 10.1016/j.isci.2026.116485
UR - https://doi.org/10.1016/j.isci.2026.116485
LA - en
ER -

CSL-JSON

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