Julienne L. Carstens, Santhoshi N. Krishnan, Arvind Rao, Anna G. Sorace, Erin H. Seeley, Sammy Ferri-Borgogno, Jared K. Burks
{"title":"Author Correction: Spatial multiplexing and omics","authors":"Julienne L. Carstens, Santhoshi N. Krishnan, Arvind Rao, Anna G. Sorace, Erin H. Seeley, Sammy Ferri-Borgogno, Jared K. Burks","doi":"10.1038/s43586-024-00352-0","DOIUrl":"10.1038/s43586-024-00352-0","url":null,"abstract":"","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":50.1,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00352-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142117972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Microbial electrodes","authors":"Annemiek Ter Heijne, Falk Harnisch","doi":"10.1038/s43586-024-00332-4","DOIUrl":"10.1038/s43586-024-00332-4","url":null,"abstract":"Microorganisms interacting with electrodes are at the centre of the evolving research field of microbial electrochemical technologies. The interdisciplinarity of the topic of microbial electrodes, including electrochemistry, microbiology and engineering, provides exciting opportunities and poses challenges. For further consolidation of the field, a solid methodology and approach as well as reporting are required. In this Primer, we provide an overview of the key parameters and main electrochemical methods, and the insights that can be obtained from microbial electrodes. These are exemplified and discussed for two case studies, one related to bioanodes and one related to biocathodes. The main applications of microbial electrodes, as well as challenges and directions for research, are summarized. Microbial electrodes combine electroactive microorganisms with electron-conducting materials to facilitate the conversion between electrical and chemical energy. In this Primer, ter Heijne and Harnisch overview the key parameters and main electrochemical methods used for characterization of microbial electrodes.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-16"},"PeriodicalIF":50.1,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142091172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Charlotte Bunne, Geoffrey Schiebinger, Andreas Krause, Aviv Regev, Marco Cuturi
{"title":"Optimal transport for single-cell and spatial omics","authors":"Charlotte Bunne, Geoffrey Schiebinger, Andreas Krause, Aviv Regev, Marco Cuturi","doi":"10.1038/s43586-024-00334-2","DOIUrl":"10.1038/s43586-024-00334-2","url":null,"abstract":"High-throughput single-cell profiling provides an unprecedented ability to uncover the molecular states of millions of cells. These technologies are, however, destructive to cells and tissues, raising practical challenges when aiming to track dynamic biological processes. As the same cell cannot be observed at multiple time points, as it changes in time and space in response to a stimulus or perturbation, these large-scale measurements only produce unaligned data sets. In this Primer, we show how such challenges can be effectively addressed using the unifying framework of optimal transport theory and tackled using the many algorithms that have been proposed for the range of scenarios of key interest in computational biology. We further review recent advances integrating optimal transport and deep learning that allow forecasting heterogeneous cellular dynamics and behaviour, crucial in particular for pressing problems in personalized medicine. The optimal transport mathematical framework can be used to describe how source populations, such as populations of single cells, can morph into another target population. In this Primer, Bunne et al. describe how optimal transport theory is used for analysing single-cell data.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-21"},"PeriodicalIF":50.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141980517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Optimal transport for single-cell and spatial omics","authors":"","doi":"10.1038/s43586-024-00345-z","DOIUrl":"10.1038/s43586-024-00345-z","url":null,"abstract":"This PrimeView highlights the versatility of optimal transport for studying single-cell and spatial omics, enabling integration of various data types into a single model and prediction of cell dynamics and treatment outcomes.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":50.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00345-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141980518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gražvydas Lukinavičius, Jonatan Alvelid, Rūta Gerasimaitė, Carmen Rodilla-Ramirez, Văn Thắng Nguyễn, Giuseppe Vicidomini, Francesca Bottanelli, Kyu Young Han, Ilaria Testa
{"title":"Stimulated emission depletion microscopy","authors":"Gražvydas Lukinavičius, Jonatan Alvelid, Rūta Gerasimaitė, Carmen Rodilla-Ramirez, Văn Thắng Nguyễn, Giuseppe Vicidomini, Francesca Bottanelli, Kyu Young Han, Ilaria Testa","doi":"10.1038/s43586-024-00335-1","DOIUrl":"10.1038/s43586-024-00335-1","url":null,"abstract":"In this Primer, we focus on the most recent advancements in stimulated emission depletion (STED) microscopy, encompassing optics, computational microscopy and probes design, which enable STED imaging to open new observation windows in challenging samples such as living cells and tissues. We showcase applications in which STED data have been essential to gain new biological insights in various cell types and model systems. Finally, we discuss what standardization will be important in our view to further advance STED imaging, including open and shareable software, analysis pipelines, data repositories and sample preparation protocols. Stimulated emission depletion microscopy opens new observation windows in challenging samples such as living cells and tissues. In this Primer, Lukinavičius et al. discuss 2D and 3D stimulated emission depletion setup, including adaptive optical elements and their combination with fluorescence lifetime techniques.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-22"},"PeriodicalIF":50.1,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141939701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Julienne L. Carstens, Santhoshi N. Krishnan, Arvind Rao, Anna G. Sorace, Erin H. Seeley, Sammy Ferri-Borgogno, Jared K. Burks
{"title":"Spatial multiplexing and omics","authors":"Julienne L. Carstens, Santhoshi N. Krishnan, Arvind Rao, Anna G. Sorace, Erin H. Seeley, Sammy Ferri-Borgogno, Jared K. Burks","doi":"10.1038/s43586-024-00330-6","DOIUrl":"10.1038/s43586-024-00330-6","url":null,"abstract":"Much like solving a game of Clue, understanding physiological mysteries involves answering who, what, when and where. Multiomics approaches delve into cellular and molecular identities (the who and what), whereas longitudinal data collection addresses the when. Spatial dimensions address the where. This Primer discusses current technologies enabling quantification across biological scales, emphasizing the importance of retaining the spatial dimension of that data. We outline experimental design considerations, including targeted versus untargeted approaches, sample types, biological scale and four main classes of molecule detection. Spatial analytics are explored, covering questioning approaches, analytical platforms, image segmentation and sampling. Example applications, reproducibility considerations, limitations and our outlook for the future are provided. Our goal is to unite spatial platforms and biological scales that not commonly brought together to encourage collaboration and innovation between diverse biological fields, offering a conceptional framework and an apples-to-apples comparison for understanding major technologies to foster cross-disciplinary dialogue. Spatial multiomics is an interdisciplinary field combining all molecular omics using advanced imaging techniques to explore interactions within tissues and cells. In this Primer, Carstens et al. examine current technologies for quantification across biological scales and discuss considerations for establishing cross-disciplinary projects.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-19"},"PeriodicalIF":50.1,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141886718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Whole-brain modelling: an essential tool for understanding brain dynamics","authors":"Gustavo Patow, Ignacio Martin, Yonatan Sanz Perl, Morten L. Kringelbach, Gustavo Deco","doi":"10.1038/s43586-024-00336-0","DOIUrl":"10.1038/s43586-024-00336-0","url":null,"abstract":"Whole-brain modelling is an essential tool that provides relevant insights for neuroscientists as they work to discover the fundamental principles of healthy brain function.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-2"},"PeriodicalIF":50.1,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141886649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Spatial multiplexing and omics","authors":"","doi":"10.1038/s43586-024-00342-2","DOIUrl":"10.1038/s43586-024-00342-2","url":null,"abstract":"This PrimeView highlights the challenges of analyzing multiplexed data for spatial omics studies.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":50.1,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00342-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141880500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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