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Protocol for quality control screening of brain organoid morphology.

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The authors' code

Markdown · 53 lines · 3.5 KB · no license

  2. # Organoid Morphology
  3. [![DOI](https://zenodo.org/badge/687934497.svg)](https://zenodo.org/badge/latestdoi/687934497)
  5. This repository contains an ImageJ 1 macro that analyses the morphology of brain organoids slices acquired in brightfiled microscopy.
  7. ![B8-kit-day18-2](https://github.com/jboulanger/Organoid_morphology/assets/3415561/1be0f509-007b-4457-966d-0f7a09be3281)
  9. The segmented contour is analyzed to extract several parameters:
  10. - Area [um^2]: Area of the selection in um^2 ("Area" measurement)
  11. - Perimeter [um]: Perimeter of the selection ("Perim." measurement)
  12. - Average Radius [um]: Average distance R0 of the contour to the center of the selection
  13. - Roundess: 4 x [Area/π (Major axis)2] ("Round" measurement)
  14. - Aspect Ratio: Major axis / Minor axis of the fitted ellipse ("AR" measurement)
  15. - Feret [um]: the longest distance between any two points along the selection boundary ("Feret" Measurement)
  16. - Min Feret [um]: the minimum distance between any two points along the selection boundary ("MinFeret" Measurement)
  17. - Circularity: 4π x (Area/Perimeter^2) ("Circ." Measurement)
  18. - Inflection points: number of detected inflection points
  19. - Weighted curvature [um^-1] : Logarithm of the sum of the squared curvature x segment length
  20. - DNE: logarithm of the square of the variation of the normal n=(dy,-dx) of the contour projected on its tangent t=(dx,dy) where dx and dy are the first derivative in x and y. DNE is normalised by the average radius (R0).
  21. - Transparency: the mean response of the Laplacian of Gaussian (LoG) filter.
  22. - Mean curvature [um^-1]: Average of the curvature along the contour
  23. - Std curvature: Standard deviation of the curvature along the contour
  24. - R0 x Std curvature: Standard deviation of the curvature along the contour normalized by the average radius (R0)
  26. The curvature along the contour is the inverse of the radius of the osculating circle and is computed as [(dx * dyy) – (dy * dxx)] / [(dx^2) + (dy^2)]^3/2 where dx and dy are the first derivative in x and y and dxx and dyy are the second derivative of the contour. The curvature is computed with a [geometric approach](https://scholar.rose-hulman.edu/cgi/viewcontent.cgi?article=1233&context=rhumj) using Heron's formula.
  30. ## Installation
  31. Download the macro [Organoid_Morphology.ijm](https://raw.githubusercontent.com/jboulanger/Organoid_morphology/main/Organoid_Morphology.ijm).
  33. ## Usage
  34. Open the macro in the script editor and press either Run or Batch.
  36. - The input file must be a TIFF file with a valid pixel calibration in microns.
  37. - Select manual selection if a manual segmentation is preferred
  38. - Overlay: select the measure to overlay with the image
  39. - Display Info: select this to display additional information as an overlay on the image
  40. - Add colorbar: select this to display a color bar to the selected measure
  41. - Colorbar min: set the minimum value of the colorbar
  42. - Colorbar max: set the maximum value of the colorbar
  43. - Save image as jpeg and close: select this to save the image as a jpg file with the annotations (contour, info, colorbar, etc)
  44. - Use Saved ROI: select this to use previoulsy stored ROI (filename.zip -> filename.roi)
  45. - Marker scale: define the scale of the marker for the inflection points
  47. Measurements are appended into a single table.
  49. A typical workflow would require to process many images running the macro using "Batch" and saving jpg and roi files.
  50. Inspect the jpeg file to identify the poorly segmented file and correct those with a manual segmentation step to update the jpeg and roi file.
  51. Finally, run again the macro on all files with the option "Use Saved ROI" enabled.

README.md at commit 282cd22, no license · at the source

Overview

Authors: Ilaria Chiaradia1, Jerome Boulanger1, Sofie Blomberg Elmkvist2, Martin Røssel Larsen2, Madeline A. Lancaster1
ORCID iDs: Ilaria Chiaradia, Sofie Blomberg Elmkvist, Madeline A. Lancaster
  1. MRC LMB, CB2 0QH Cambridge, UK
  2. Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
Institutions: MRC Laboratory of Molecular Biology (United Kingdom); University of Southern Denmark (Denmark)
Journal: STAR protocols, volume 7, issue 1, article 104423
Dates: published online 13 March 2026; in print March 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1016/j.xpro.2026.104423 · PMID 41863793 · PMCID PMC12990332 · OpenAlex W7135038030
Open access: gold, a free copy (OpenAlex)
Status: empty repository
Categories: human (organism), developmental (subfield)
Methods: Smoothing, state filtering, decompositions, Machine learning, fMRI & imaging
Keywords: Developmental biology, Stem Cells, Organoids
MeSH: Brain*, Image Processing, Computer-Assisted*, Organoids*, Animals, Humans, Quality Control (* major topic)
Topic: Glioma Diagnosis and Treatment (Genetics, Medicine), according to OpenAlex
Funding: UK Medical Research Council (MC_UP_1201/9); EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council) (STG 757710)
Citations: not cited yet (Europe PMC); 29 references in the paper

Abstract

Neural organoids can exhibit variability in both tissue shape and tissue identity. Here, we present a pipeline for rapid, protocol-agnostic quality control screening of brain organoids based on their overall gross morphology. We describe a semi-automated image analysis of organoid size, shape, and texture from 2D bright-field imaging. We provide a reference dataset of brain organoids with complex morphology. We show how to integrate input and reference organoids and perform the unbiased sample selection by k-means clustering.

For complete details on the use and execution of this protocol, please refer to Chiaradia et al.1

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

Repository

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

jboulanger/Organoid_morphology

License: none: the authors keep all their rights
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: 282cd226732e7d7b702dfcfb06a2d1f8ff28b5ff, 21 March 2024
Size: 3 files, 0 scripts
Software Heritage: not archived
Found in: “Data and code availability”
Holds: README, CITATION.cff
Not found: license file, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
1 file
At the source: github.com/jboulanger/Organoid_morphology

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

Tracing map

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  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 0 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
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Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Data and code availability

• The reference dataset for Figures 2 and S3–S5 in the paper is available at Zenodo Data: https://zenodo.org/records/16311731?preview=1&token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6IjBmNDU1YjY0LTAwNzUtNDY0Ny04MjdjLTMwN2UzMjFkZjIxOCIsImRhdGEiOnt9LCJyYW5kb20iOiI3MTQ4MzFkNWRiOGM2ZWU0ZDA4MmVmODc5MTM4ZWNmOCJ9.oRuLeB9xVoDqS6-3sYq30VMc0oGUrZ_XJSWhZ-acRcuZ8L1CEejmWdxBo8PSWwFV9IV2_N-hOszV_Fstg5iMBA and https://zenodo.org/records/16312269?preview=1&token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6IjEzY2IwMjI1LWI3NjEtNGFmMi1hNzY5LTM5NGI4OWUzYmQ3ZiIsImRhdGEiOnt9LCJyYW5kb20iOiI1M2ZkZDlmNjEyZjlkMjNmZDdmNjhlYWNmYmFlY2YzNSJ9.AzeNBWO2UlekRC_dXMBbKyBULPkFeVWIu8ZL3QwEwHfcW1y9KE02sgpCc2EDV52kJzMaeTiQVX05OcBcE43yNA and is publicly available as of the date of publication. • Codes generated during this study are available at Github Data: https://github.com/jboulanger/Organoid_morphology and are publicly available as of the date of publication. • Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request. • The published article includes datasets/code generated and analyzed in Chiaradia et al.1

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

Versions

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Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 3 keywords, 6 MeSH terms, 2 funders, 29 references.

Cite

This paper

Chiaradia, I., Boulanger, J., Elmkvist, S. B., Larsen, M. R., & Lancaster, M. A. (2026). Protocol for quality control screening of brain organoid morphology. STAR protocols, 7(1), 104423. https://doi.org/10.1016/j.xpro.2026.104423

BibTeX

@article{chiaradia2026protocol,
author = {Chiaradia, Ilaria and Boulanger, Jerome and Elmkvist, Sofie Blomberg and Larsen, Martin Røssel and Lancaster, Madeline A.},
title = {{Protocol for quality control screening of brain organoid morphology}},
journal = {STAR protocols},
year = {2026},
month = mar,
volume = {7},
number = {1},
pages = {104423},
publisher = {Elsevier},
issn = {2666-1667},
doi = {10.1016/j.xpro.2026.104423},
url = {https://doi.org/10.1016/j.xpro.2026.104423},
pmid = {41863793},
pmcid = {PMC12990332}
}

RIS

TY - JOUR
AU - Chiaradia, Ilaria
AU - Boulanger, Jerome
AU - Elmkvist, Sofie Blomberg
AU - Larsen, Martin Røssel
AU - Lancaster, Madeline A.
TI - Protocol for quality control screening of brain organoid morphology
T2 - STAR protocols
J2 - STAR Protoc
PY - 2026
DA - 2026/03/13
VL - 7
IS - 1
SP - 104423
SN - 2666-1667
PB - Elsevier
DO - 10.1016/j.xpro.2026.104423
UR - https://doi.org/10.1016/j.xpro.2026.104423
LA - en
ER -

CSL-JSON

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