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We present ConeMapper, an open-source MATLAB software that integrates a fully convolutional neural network (FCN) for the automatic detection and analysis of cone photoreceptors in confocal adaptive optics scanning light ophthalmoscopy (AOSLO) images of the foveal center. The FCN was trained on a dataset of 49 healthy retinas and showed improved performance over previously published neural networks, particularly in the central fovea, achieving an <jats:inline-formula>\n              <jats:tex-math>$$F_1$$<\/jats:tex-math>\n            <\/jats:inline-formula> score of 0.9769 across the validation set, critically reducing analysis time. In addition to automatic cone detection, ConeMapper provides efficient manual annotation tools, visualizations and topographical analysis, offering users detailed metrics for further analysis. ConeMapper is freely available, with ongoing development aimed at enhancing functionality and adaptability to different retinal imaging modalities.<\/jats:p>","DOI":"10.1038\/s41598-025-08028-9","type":"journal-article","created":{"date-parts":[[2025,7,4]],"date-time":"2025-07-04T01:38:10Z","timestamp":1751593090000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Neural network assisted annotation and analysis tool to study in-vivo foveolar cone photoreceptor topography"],"prefix":"10.1038","volume":"15","author":[{"given":"Aleksandr","family":"Gutnikov","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick","family":"H\u00e4hn-Schumacher","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julius","family":"Ameln","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shekoufeh Gorgi","family":"Zadeh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Schultz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wolf","family":"Harmening","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,7,4]]},"reference":[{"key":"8028_CR1","doi-asserted-by":"publisher","first-page":"1413","DOI":"10.1038\/nn.4622","volume":"20","author":"M Poletti","year":"2017","unstructured":"Poletti, M., Rucci, M. & Carrasco, M. 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