{"title":"MitoSeg: Mitochondria segmentation tool","authors":"Faris Serdar Taşel , Efe Çi̇ftci̇","doi":"10.1016/j.softx.2025.102081","DOIUrl":null,"url":null,"abstract":"<div><div>Recent studies suggest a potential link between the physical structure of mitochondria and neurodegenerative diseases. With advances in Electron Microscopy techniques, it has become possible to visualize the boundary and cristae structures of mitochondria in detail. Segmenting mitochondria from microscopy images remains challenging due to image quality and complex morphology of mitochondria, including cristae and the other subcellular structures. It is crucial to automatically segment mitochondria from images exhibiting different mitochondrial boundary and crista characteristics to investigate the relationship between mitochondria and diseases. In this paper, we present a software solution for mitochondrial segmentation using an automatic validation scheme based on the general physical properties of mitochondria, highlighting boundaries in electron microscopy tomography images and generating corresponding 3D meshes. These capabilities help researchers conduct further investigations into mitochondrial morphology and explore its role in the mechanisms of neurodegenerative diseases.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"30 ","pages":"Article 102081"},"PeriodicalIF":2.4000,"publicationDate":"2025-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"SoftwareX","FirstCategoryId":"94","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2352711025000482","RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"COMPUTER SCIENCE, SOFTWARE ENGINEERING","Score":null,"Total":0}
引用次数: 0
Abstract
Recent studies suggest a potential link between the physical structure of mitochondria and neurodegenerative diseases. With advances in Electron Microscopy techniques, it has become possible to visualize the boundary and cristae structures of mitochondria in detail. Segmenting mitochondria from microscopy images remains challenging due to image quality and complex morphology of mitochondria, including cristae and the other subcellular structures. It is crucial to automatically segment mitochondria from images exhibiting different mitochondrial boundary and crista characteristics to investigate the relationship between mitochondria and diseases. In this paper, we present a software solution for mitochondrial segmentation using an automatic validation scheme based on the general physical properties of mitochondria, highlighting boundaries in electron microscopy tomography images and generating corresponding 3D meshes. These capabilities help researchers conduct further investigations into mitochondrial morphology and explore its role in the mechanisms of neurodegenerative diseases.
期刊介绍：
SoftwareX aims to acknowledge the impact of software on today''s research practice, and on new scientific discoveries in almost all research domains. SoftwareX also aims to stress the importance of the software developers who are, in part, responsible for this impact. To this end, SoftwareX aims to support publication of research software in such a way that: The software is given a stamp of scientific relevance, and provided with a peer-reviewed recognition of scientific impact; The software developers are given the credits they deserve; The software is citable, allowing traditional metrics of scientific excellence to apply; The academic career paths of software developers are supported rather than hindered; The software is publicly available for inspection, validation, and re-use. Above all, SoftwareX aims to inform researchers about software applications, tools and libraries with a (proven) potential to impact the process of scientific discovery in various domains. The journal is multidisciplinary and accepts submissions from within and across subject domains such as those represented within the broad thematic areas below: Mathematical and Physical Sciences; Environmental Sciences; Medical and Biological Sciences; Humanities, Arts and Social Sciences. Originating from these broad thematic areas, the journal also welcomes submissions of software that works in cross cutting thematic areas, such as citizen science, cybersecurity, digital economy, energy, global resource stewardship, health and wellbeing, etcetera. SoftwareX specifically aims to accept submissions representing domain-independent software that may impact more than one research domain.
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