insideOutside: an accessible algorithm for classifying interior and exterior points, with applications in embryology Article Swipe
Stanley E. Strawbridge
,
Agata Kurowski
,
Elena Corujo-Simón
,
Alastair Fletcher
,
Jennifer Nichols
,
Alexander G. Fletcher
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1242/bio.060055
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1242/bio.060055
A crucial aspect of embryology is relating the position of individual cells to the broader geometry of the embryo. A classic example of this is the first cell-fate decision of the mouse embryo, where interior cells become inner cell mass and exterior cells become trophectoderm. Fluorescent labelling, imaging, and quantification of tissue-specific proteins have advanced our understanding of this dynamic process. However, instances arise where these markers are either not available, or not reliable, and we are left only with the cells’ spatial locations. Therefore, a simple, robust method for classifying interior and exterior cells of an embryo using spatial information is required. Here, we describe a simple mathematical framework and an unsupervised machine learning approach, termed insideOutside, for classifying interior and exterior points of a three-dimensional point-cloud, a common output from imaged cells within the early mouse embryo. We benchmark our method against other published methods to demonstrate that it yields greater accuracy in classification of nuclei from the pre-implantation mouse embryos and greater accuracy when challenged with local surface concavities. We have made MATLAB and Python implementations of the method freely available. This method should prove useful for embryology, with broader applications to similar data arising in the life sciences.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1242/bio.060055
- https://journals.biologists.com/bio/article-pdf/12/9/bio060055/3107731/bio060055.pdf
- OA Status
- gold
- Cited By
- 4
- References
- 51
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4386151511
All OpenAlex metadata
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https://openalex.org/W4386151511Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1242/bio.060055Digital Object Identifier
- Title
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insideOutside: an accessible algorithm for classifying interior and exterior points, with applications in embryologyWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2023Year of publication
- Publication date
-
2023-08-25Full publication date if available
- Authors
-
Stanley E. Strawbridge, Agata Kurowski, Elena Corujo-Simón, Alastair Fletcher, Jennifer Nichols, Alexander G. FletcherList of authors in order
- Landing page
-
https://doi.org/10.1242/bio.060055Publisher landing page
- PDF URL
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https://journals.biologists.com/bio/article-pdf/12/9/bio060055/3107731/bio060055.pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://journals.biologists.com/bio/article-pdf/12/9/bio060055/3107731/bio060055.pdfDirect OA link when available
- Concepts
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Embryology, Biology, Embryo, Python (programming language), Artificial intelligence, Computer science, Benchmark (surveying), Algorithm, Anatomy, Bioinformatics, Cell biology, Programming language, Cartography, GeographyTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
4Total citation count in OpenAlex
- Citations by year (recent)
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2025: 2, 2024: 2Per-year citation counts (last 5 years)
- References (count)
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51Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.challenged | 168 |
| abstract_inverted_index.embryology | 5 |
| abstract_inverted_index.individual | 11 |
| abstract_inverted_index.labelling, | 47 |
| abstract_inverted_index.locations. | 84 |
| abstract_inverted_index.Fluorescent | 46 |
| abstract_inverted_index.classifying | 91, 120 |
| abstract_inverted_index.demonstrate | 149 |
| abstract_inverted_index.embryology, | 191 |
| abstract_inverted_index.information | 101 |
| abstract_inverted_index.applications | 194 |
| abstract_inverted_index.concavities. | 172 |
| abstract_inverted_index.mathematical | 109 |
| abstract_inverted_index.point-cloud, | 128 |
| abstract_inverted_index.unsupervised | 113 |
| abstract_inverted_index.understanding | 57 |
| abstract_inverted_index.classification | 156 |
| abstract_inverted_index.insideOutside, | 118 |
| abstract_inverted_index.quantification | 50 |
| abstract_inverted_index.trophectoderm. | 45 |
| abstract_inverted_index.implementations | 179 |
| abstract_inverted_index.tissue-specific | 52 |
| abstract_inverted_index.pre-implantation | 161 |
| abstract_inverted_index.three-dimensional | 127 |
| cited_by_percentile_year.max | 97 |
| cited_by_percentile_year.min | 94 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 6 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/12 |
| sustainable_development_goals[0].score | 0.47999998927116394 |
| sustainable_development_goals[0].display_name | Responsible consumption and production |
| citation_normalized_percentile.value | 0.73177987 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |