{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T13:16:23Z","timestamp":1785417383408,"version":"3.56.0"},"posted":{"date-parts":[[2025,7,31]]},"group-title":"Developmental Biology","reference-count":44,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,7,31]],"date-time":"2025-07-31T00:00:00Z","timestamp":1753920000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"award":["2150280"],"award-info":[{"award-number":["2150280"]}],"id":[{"id":"https:\/\/ror.org\/021nxhr62","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R35GM15078"],"award-info":[{"award-number":["R35GM15078"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"crossref","award":["R01GM152810"],"award-info":[{"award-number":["R01GM152810"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,7,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>Developing tissues reproduce nearly identical patterns from animal to animal, despite the process being stochastic at the cell level. A major challenge for researchers is the ability to quantify and classify complex cell and tissue spot patterns across wild type and perturbed conditions. Here, we use the organization of small sensory bristles on the fruit fly thorax as a model system to address this problem. A well-known and easily observable distinguishing feature of spot patterns is density. Beyond this, it is unclear how to quantitatively distinguish between patterns in a reproducible way. Our work evaluates the utility of the spatial clustering of spot patterns in quantifying their organization. We propose four clustering features, obtained using the density-based spatial clustering of applications with noise (DBSCAN) algorithm. Together with pattern density we assess how these features can quantify and distinguish between bristle patterns in a variety of wild-type and mutant flies to confirm known perturbations and discover new ones. Our results show that a combination of spot pattern density and the variance between the size of clusters is sufficient to distinguish between 70% of patterns from wild-type and mutant tissues.<\/jats:p>","DOI":"10.1101\/2025.07.29.667315","type":"posted-content","created":{"date-parts":[[2025,7,31]],"date-time":"2025-07-31T17:45:15Z","timestamp":1753983915000},"source":"Crossref","is-referenced-by-count":0,"title":["Quantifying bristle cell organization in\n                  <i>Drosophila melanogaster<\/i>\n                  using spatial clustering features"],"prefix":"10.64898","author":[{"given":"Wisdom K.","family":"Attipoe","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Audrey","family":"Neighmond","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oakley","family":"Waters","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.H Dinuka Sewwandi","family":"De Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7022-9482","authenticated-orcid":false,"given":"Ginger L.","family":"Hunter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4710-8006","authenticated-orcid":false,"given":"Emmanuel","family":"Asante-Asamani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025080116051764000_2025.07.29.667315v1.1","doi-asserted-by":"publisher","DOI":"10.1242\/dev.109.3.509"},{"key":"2025080116051764000_2025.07.29.667315v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/nrm.2016.94"},{"key":"2025080116051764000_2025.07.29.667315v1.3","doi-asserted-by":"publisher","DOI":"10.1242\/dev.172148"},{"key":"2025080116051764000_2025.07.29.667315v1.4","doi-asserted-by":"publisher","DOI":"10.1126\/science.aai7407"},{"key":"2025080116051764000_2025.07.29.667315v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2010.06.006"},{"key":"2025080116051764000_2025.07.29.667315v1.6","doi-asserted-by":"publisher","DOI":"10.1006\/jtbi.1996.0233"},{"key":"2025080116051764000_2025.07.29.667315v1.7","doi-asserted-by":"publisher","DOI":"10.1038\/nature02157"},{"issue":"124","key":"2025080116051764000_2025.07.29.667315v1.8","doi-asserted-by":"crossref","first-page":"20160484","DOI":"10.1098\/rsif.2016.0484","article-title":"A new mechanism for spatial pattern formation via lateral and protrusion-mediated lateral signalling","volume":"13","year":"2016","journal-title":"Journal of the Royal Society Interface"},{"key":"2025080116051764000_2025.07.29.667315v1.9","doi-asserted-by":"publisher","DOI":"10.1242\/jcs.060772"},{"key":"2025080116051764000_2025.07.29.667315v1.10","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.ydbio.2023.11.002","article-title":"Myosin xv is a negative regulator of signaling filopodia during long-range lateral inhibition","volume":"505","year":"2024","journal-title":"Developmental Biology"},{"key":"2025080116051764000_2025.07.29.667315v1.11","doi-asserted-by":"crossref","unstructured":"J. L. Salazar , S. Yamamoto , Integration of drosophila and human genetics to understand notch signaling related diseases, Molecular Mechanisms of Notch Signaling (2018) 141\u2013185.","DOI":"10.1007\/978-3-319-89512-3_8"},{"key":"2025080116051764000_2025.07.29.667315v1.12","doi-asserted-by":"publisher","DOI":"10.1152\/physrev.00005.2017"},{"key":"2025080116051764000_2025.07.29.667315v1.13","doi-asserted-by":"publisher","DOI":"10.1038\/nature07936"},{"issue":"1","key":"2025080116051764000_2025.07.29.667315v1.14","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1093\/genetics\/150.1.211","article-title":"A genetic screen for novel components of the notch signaling pathway during drosophila bristle development","volume":"150","year":"1998","journal-title":"Genetics"},{"key":"2025080116051764000_2025.07.29.667315v1.15","doi-asserted-by":"crossref","unstructured":"C. Hennig , M. Meila , F. Murtagh , R. Rocci , Handbook of cluster analysis, CRC press, 2015.","DOI":"10.1201\/b19706"},{"key":"2025080116051764000_2025.07.29.667315v1.16","doi-asserted-by":"crossref","unstructured":"T. Hastie , R. Tibshirani , J. H. Friedman , J. H. Friedman , The elements of statistical learning: data mining, inference, and prediction, Vol. 2, Springer, 2009.","DOI":"10.1007\/978-0-387-84858-7"},{"issue":"8","key":"2025080116051764000_2025.07.29.667315v1.17","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.3390\/electronics9081295","article-title":"The k-means algorithm: A comprehensive survey and performance evaluation","volume":"9","year":"2020","journal-title":"Electronics"},{"key":"2025080116051764000_2025.07.29.667315v1.18","first-page":"226","volume":"96","year":"1996","journal-title":"A density-based algorithm for discovering clusters in large spatial databases with noise, in: kdd"},{"key":"2025080116051764000_2025.07.29.667315v1.19","doi-asserted-by":"crossref","first-page":"107175","DOI":"10.1016\/j.bspc.2024.107175","article-title":"Segmentation of coronary arteries from x-ray angiographic images using density based spatial clustering of applications with noise (dbscan)","volume":"101","year":"2025","journal-title":"Biomedical Signal Processing and Control"},{"issue":"1","key":"2025080116051764000_2025.07.29.667315v1.20","doi-asserted-by":"crossref","first-page":"18868","DOI":"10.1038\/s41598-023-45190-4","article-title":"Extended methods for spatial cell classification with dbscan-cellx","volume":"13","author":"L. K\u00fcchenhoff,","year":"2023","journal-title":"Scientific Reports"},{"issue":"1","key":"2025080116051764000_2025.07.29.667315v1.21","first-page":"4","article-title":"Gene expression analysis via spatial clustering and evaluationindexing","volume":"4","year":"2023","journal-title":"Iraqi Journal for Computer Science and Mathematics"},{"issue":"3","key":"2025080116051764000_2025.07.29.667315v1.22","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/j.cmpb.2010.12.012","article-title":"Simulation of dna damage clustering after proton irradiation using an adapted dbscan algorithm","volume":"101","year":"2011","journal-title":"Computer methods and programs in biomedicine"},{"key":"2025080116051764000_2025.07.29.667315v1.23","doi-asserted-by":"publisher","DOI":"10.1006\/dbio.1997.8707"},{"key":"2025080116051764000_2025.07.29.667315v1.24","doi-asserted-by":"crossref","unstructured":"E. Yeh , L. Zhou , N. Rudzik , G. L. Boulianne , Neuralized functions cell autonomously to regulate drosophila sense organ development, The EMBO journal (2000).","DOI":"10.1093\/emboj\/19.17.4827"},{"issue":"2","key":"2025080116051764000_2025.07.29.667315v1.25","first-page":"401","volume":"118","year":"1993","journal-title":"Targeted gene expression as a means of altering cell fates and generating dominant phenotypes, development"},{"key":"2025080116051764000_2025.07.29.667315v1.26","doi-asserted-by":"publisher","DOI":"10.1126\/science.274.5285.252"},{"key":"2025080116051764000_2025.07.29.667315v1.27","first-page":"301","volume-title":"Monitoring notch\/delta endosomal trafficking and signaling in drosophila, in: Methods in enzymology","volume":"534","year":"2014"},{"issue":"10","key":"2025080116051764000_2025.07.29.667315v1.28","first-page":"2319","volume":"132","year":"2005","journal-title":"The ubiquitin ligase drosophila mind bomb promotes notch signaling by regulating the localization and activity of serrate and delta, development"},{"key":"2025080116051764000_2025.07.29.667315v1.29","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0030096"},{"key":"2025080116051764000_2025.07.29.667315v1.30","doi-asserted-by":"publisher","DOI":"10.1006\/dbio.2001.0482"},{"key":"2025080116051764000_2025.07.29.667315v1.31","doi-asserted-by":"publisher","DOI":"10.1016\/j.ceb.2016.10.002"},{"key":"2025080116051764000_2025.07.29.667315v1.32","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2021.04.005"},{"key":"2025080116051764000_2025.07.29.667315v1.33","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.104.026369"},{"key":"2025080116051764000_2025.07.29.667315v1.34","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abg0147"},{"key":"2025080116051764000_2025.07.29.667315v1.35","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.119.4.823"},{"key":"2025080116051764000_2025.07.29.667315v1.36","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.108.099986"},{"key":"2025080116051764000_2025.07.29.667315v1.37","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1101415108"},{"issue":"1","key":"2025080116051764000_2025.07.29.667315v1.38","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1186\/s12915-023-01759-z","article-title":"The meaning of ubiquitylation of the dsl ligand delta for the development of drosophila","volume":"21","year":"2023","journal-title":"BMC biology"},{"key":"2025080116051764000_2025.07.29.667315v1.39","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2214535120"},{"key":"2025080116051764000_2025.07.29.667315v1.40","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.200109057"},{"key":"2025080116051764000_2025.07.29.667315v1.41","doi-asserted-by":"publisher","DOI":"10.1038\/35054566"},{"key":"2025080116051764000_2025.07.29.667315v1.42","doi-asserted-by":"crossref","first-page":"e75746","DOI":"10.7554\/eLife.75746","article-title":"A neural progenitor mitotic wave is required for asynchronous axon outgrowth and morphology","volume":"11","year":"2022","journal-title":"Elife"},{"issue":"9","key":"2025080116051764000_2025.07.29.667315v1.43","doi-asserted-by":"crossref","first-page":"e0291409","DOI":"10.1371\/journal.pone.0291409","article-title":"Scabrous is distributed via signaling filopodia to modulate notch response during bristle patterning in drosophila","volume":"18","year":"2023","journal-title":"Plos one"},{"issue":"5","key":"2025080116051764000_2025.07.29.667315v1.44","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1016\/j.neuron.2018.10.005","article-title":"Alcohol activates scabrous-notch to influence associated memories","volume":"100","year":"2018","journal-title":"Neuron"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.07.29.667315","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T09:14:09Z","timestamp":1768468449000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.07.29.667315"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,31]]},"references-count":44,"URL":"https:\/\/doi.org\/10.1101\/2025.07.29.667315","relation":{},"subject":[],"published":{"date-parts":[[2025,7,31]]},"subtype":"preprint"}}