Gaëlle Letort, Léo Valon, Arthur Michaut, Tom Cumming, Laura Xénard, Minh-Son Phan, Nicolas Dray, Curtis T Rueden, François Schweisguth, Jérôme Gros, Laure Bally-Cuif, Jean-Yves Tinevez, Romain Levayer
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引用次数: 0
Abstract
Despite advances in deep-learning and bioimage analysis, manual curation of segmented and tracking data is still required to extract accurate quantitative single cell temporal information from large tissue/embryo movies. However, very few tools address specifically this challenge. We present here EpiCure (Epithelial Curation), a versatile tool designed to streamline and accelerate manual curation of segmentation and tracking in 2D movies of large epithelial tissues. EpiCure uses temporal information and morphometric parameters to automatically identify segmentation and tracking errors and provides user-friendly tools to correct them. It focuses on ergonomics and offers visualization options to help navigate movies covering a large number of cells, speeding up the detection and curation of errors. EpiCure is highly interoperable, supports input from diverse segmentation tools and includes multiple export filters enabling seamless integration with downstream analysis pipelines. Using movies from several animal models, we highlight the importance of curating cell segmentation and tracking for accurate downstream analysis, and how EpiCure helps by extracting single cell dynamics and detecting cellular events in a large dataset.
期刊介绍：
Development’s scope covers all aspects of plant and animal development, including stem cell biology and regeneration. The single most important criterion for acceptance in Development is scientific excellence. Research papers (articles and reports) should therefore pose and test a significant hypothesis or address a significant question, and should provide novel perspectives that advance our understanding of development. We also encourage submission of papers that use computational methods or mathematical models to obtain significant new insights into developmental biology topics. Manuscripts that are descriptive in nature will be considered only when they lay important groundwork for a field and/or provide novel resources for understanding developmental processes of broad interest to the community.
Development includes a Techniques and Resources section for the publication of new methods, datasets, and other types of resources. Papers describing new techniques should include a proof-of-principle demonstration that the technique is valuable to the developmental biology community; they need not include in-depth follow-up analysis. The technique must be described in sufficient detail to be easily replicated by other investigators. Development will also consider protocol-type papers of exceptional interest to the community. We welcome submission of Resource papers, for example those reporting new databases, systems-level datasets, or genetic resources of major value to the developmental biology community. For all papers, the data or resource described must be made available to the community with minimal restrictions upon publication.
To aid navigability, Development has dedicated sections of the journal to stem cells & regeneration and to human development. The criteria for acceptance into these sections is identical to those outlined above. Authors and editors are encouraged to nominate appropriate manuscripts for inclusion in one of these sections.
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