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Interneurons in the subplate are associated with cortical maturation across the foetal human cortex

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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

Python · 61 lines · 1.4 KB · no license

  1. # -*- coding: utf-8 -*-
  2. """
  3. Created on Mon Feb 2 14:16:03 2026
  5. @author: gabri
  6. """
  8. import cv2
  9. import numpy as np
  10. from skimage import filters, morphology, measure
  11. import matplotlib.pyplot as plt
  14. #input the image of SP layer of each region
  15. image_path = r"C:\Users\gabri\Desktop\images from LMD\subplate\VFC.png"
  17. IMAGE_WIDTH_UM = 343.8
  18. IMAGE_HEIGHT_UM = 272.4
  21. img = cv2.imread(image_path, cv2.IMREAD_GRAYSCALE)
  24. img = cv2.bitwise_not(img)
  25. img_blur = cv2.GaussianBlur(img, (3, 3), 0)
  27. thresh = filters.threshold_otsu(img_blur)
  28. binary = img_blur > thresh
  30. # ==============================
  31. # COUNT CONNECTED PROFILES
  34. labels = measure.label(binary, connectivity=2)
  35. profile_count = labels.max()
  38. # ==============================
  39. # WHITE : BLACK RATIO - this is the proxy for cell density white=Nissl-positive cells, black=background
  40. # ==============================
  42. white_pixels = np.sum(binary)
  43. total_pixels = binary.size
  44. signal_fraction = white_pixels / total_pixels
  46. # ==============================
  47. # OUTPUT
  48. # ==============================
  50. print(f"Nissl-positive profiles: {profile_count}")
  51. print(f"Signal fraction (white/total): {signal_fraction:.4f}")
  53. # ==============================
  54. # VISUAL QC
  55. # ==============================
  57. plt.figure(figsize=(6,6))
  58. plt.imshow(binary, cmap='gray')
  59. plt.title("Binary mask (signal = white)")
  60. plt.axis('off')
  61. plt.show()

count cell proportion.py, no license · at the source

Overview

Authors: Gabriela Epihova1, Duncan Astle1
  1. MRC Cognition and Brain Sciences Unit
Institutions: MRC Cognition and Brain Sciences Unit (United Kingdom)
Journal: Research Square (preprint)
Dates: published 5 August 2026
Type: Preprint
License: CC BY
Identifiers: DOI 10.21203/rs.3.rs-10335768/v1 · OpenAlex W7172530624
Open access: green, a free copy (OpenAlex)
Preprint: osf.io/8s6ka
Status: code verified
Categories: human (organism), developmental (subfield)
Methods: Spectral & time-frequency
Keywords: interneurons, foetal neurodevelopment, fronto-temporal cortex, cortical maturation
Topic: Neurogenesis and neuroplasticity mechanisms (Developmental Neuroscience, Neuroscience), according to OpenAlex
Funding: James S. McDonnell Foundation; National Institute for Health and Care Research ((NIHR203312); Templeton World Charity Foundation (MC-A0606-5PQ41, TWCF-2022-30510, 501100011730, DOI 501100011730); Medical Research Council (MC‐A0606‐5PQ41, NIHR203312); NIHR Cambridge Biomedical Research Centre (NIHR 203312)
Citations: not cited yet (OpenAlex); 35 references in the paper

Abstract

GABA is the principle excitatory neurotransmitter of the foetal brain. This early excitatory role is driven by developing GABAergic interneurons, whose spatial distribution and maturation influence regional cortical development. Here, we leveraged brain transcriptomes from human foetal brains to investigate early regional differences in interneuron expression and identify the functional programmes associated with this spatial pattern. Across the entire second and third trimesters the expression of interneuron marker genes was higher in frontal and temporal cortical regions, relative to parietal and occipital cortex. This topographic preference was evident across all non-proliferative transient layers of the foetal cortex – the cortical plate, subplate and intermediate zone. Across the cortex interneuron expression within the subplate was associated with upregulation of genes related to neural development and maturation. Importantly, this relationship was specific to the subplate, as interneuron expression in other transient layers was not associated with enrichment in these programmes. Further, the levels of interneuron expression across cortical regions were not associated with morphological subplate measures of thickness and cellular density, which instead reflected neuronal migration rates. Together, these results underscore the synchrony between interneuron expression and neuronal maturation across the developing foetal cortex.

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

Repository

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

OSF 8s6ka

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Languages: Python (3)
Size: 29 files, 3 scripts
Software Heritage: not checked
Found in: “Data availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Matplotlib (2 files), NumPy (2 files), pandas (2 files), OpenCV (1 file), scikit-image (1 file), scikit-learn (1 file), SciPy (1 file), seaborn (1 file), statsmodels (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
3 files
At the source: osf.io/8s6ka

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:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 3 scripts, 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

Datasets cited

Data availability

Data and codes from the current project are publicly available at https://osf.io/8s6ka.

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

Versions

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Version 3, 28 September 2026

  • Funding: added James S. McDonnell Foundation; National Institute for Health and Care Research: (NIHR203312; Templeton World Charity Foundation: MC-A0606-5PQ41, TWCF-2022-30510, 501100011730, DOI 501100011730; Medical Research Council: MC‐A0606‐5PQ41, NIHR203312; NIHR Cambridge Biomedical Research Centre: NIHR 203312

Version 1, 27 September 2026: the first record

Recorded: type, journal, 2 authors, 4 keywords, 34 references.

Cite

This paper

Epihova, G., & Astle, D. (2026). Interneurons in the subplate are associated with cortical maturation across the foetal human cortex. Research Square (preprint). https://doi.org/10.21203/rs.3.rs-10335768/v1

BibTeX

@article{epihova2026interneurons,
author = {Epihova, Gabriela and Astle, Duncan},
title = {{Interneurons in the subplate are associated with cortical maturation across the foetal human cortex}},
journal = {Research Square (preprint)},
year = {2026},
month = aug,
publisher = {Research Square},
issn = {2693-5015},
doi = {10.21203/rs.3.rs-10335768/v1},
url = {https://doi.org/10.21203/rs.3.rs-10335768/v1}
}

RIS

TY - JOUR
AU - Epihova, Gabriela
AU - Astle, Duncan
TI - Interneurons in the subplate are associated with cortical maturation across the foetal human cortex
T2 - Research Square (preprint)
J2 - Res Sq
PY - 2026
DA - 2026/08/05
SN - 2693-5015
PB - Research Square
DO - 10.21203/rs.3.rs-10335768/v1
UR - https://doi.org/10.21203/rs.3.rs-10335768/v1
ER -

CSL-JSON

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"type": "article",
"title": "Interneurons in the subplate are associated with cortical maturation across the foetal human cortex",
"container-title": "Research Square (preprint)",
"author": [
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"family": "Epihova",
"given": "Gabriela"
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"container-title-short": "Res Sq",
"DOI": "10.21203/rs.3.rs-10335768/v1",
"ISSN": "2693-5015",
"publisher": "Research Square",
"URL": "https://doi.org/10.21203/rs.3.rs-10335768/v1",
"issued": {
"date-parts": [
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8,
5
]
]
}
}

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