Nature Methods最新文献_第9页

Conference networking: posters, talks, conversations 会议网络：海报，演讲，对话。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-01-02 DOI: 10.1038/s41592-024-02566-2

Vivien Marx

引用次数: 0

Vibrational fiber photometry: label-free and reporter-free minimally invasive Raman spectroscopy deep in the mouse brain 振动纤维光度法：无标签和无报告的小鼠脑深部微创拉曼光谱。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-31 DOI: 10.1038/s41592-024-02557-3

Filippo Pisano, Mariam Masmudi-Martín, Maria Samuela Andriani, Elena Cid, Mohammadrahim Kazemzadeh, Marco Pisanello, Antonio Balena, Liam Collard, Teresa Jurado Parras, Marco Bianco, Patricia Baena, Francesco Tantussi, Marco Grande, Leonardo Sileo, Francesco Gentile, Francesco De Angelis, Massimo De Vittorio, Liset Menendez de la Prida, Manuel Valiente, Ferruccio Pisanello

{"title":"Vibrational fiber photometry: label-free and reporter-free minimally invasive Raman spectroscopy deep in the mouse brain","authors":"Filippo Pisano, Mariam Masmudi-Martín, Maria Samuela Andriani, Elena Cid, Mohammadrahim Kazemzadeh, Marco Pisanello, Antonio Balena, Liam Collard, Teresa Jurado Parras, Marco Bianco, Patricia Baena, Francesco Tantussi, Marco Grande, Leonardo Sileo, Francesco Gentile, Francesco De Angelis, Massimo De Vittorio, Liset Menendez de la Prida, Manuel Valiente, Ferruccio Pisanello","doi":"10.1038/s41592-024-02557-3","DOIUrl":"10.1038/s41592-024-02557-3","url":null,"abstract":"Optical approaches to monitor neural activity are transforming neuroscience, owing to a fast-evolving palette of genetically encoded molecular reporters. However, the field still requires robust and label-free technologies to monitor the multifaceted biomolecular changes accompanying brain development, aging or disease. Here, we have developed vibrational fiber photometry as a low-invasive method for label-free monitoring of the biomolecular content of arbitrarily deep regions of the mouse brain in vivo through spontaneous Raman spectroscopy. Using a tapered fiber probe as thin as 1 µm at its tip, we elucidate the cytoarchitecture of the mouse brain, monitor molecular alterations caused by traumatic brain injury, as well as detect markers of brain metastasis with high accuracy. We view our approach, which introduces a deep learning algorithm to suppress probe background, as a promising complement to the existing palette of tools for the optical interrogation of neural function, with application to fundamental and preclinical investigations of the brain and other organs. Vibrational fiber photometry enables Raman spectroscopy in the mouse brain with low impact, owing to the use of tapered fibers.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"371-379"},"PeriodicalIF":36.1,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142910033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Isotropic 100-nm resolution live-cell imaging with 4Pi-SIM 使用4Pi-SIM进行各向同性100纳米分辨率活细胞成像。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-30 DOI: 10.1038/s41592-024-02514-0

引用次数: 0

Elucidating subcellular architecture and dynamics at isotropic 100-nm resolution with 4Pi-SIM 利用4Pi-SIM在各向同性100纳米分辨率下阐明亚细胞结构和动力学。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-23 DOI: 10.1038/s41592-024-02515-z

Zijing Ouyang, Qian Wang, Xiaoyu Li, Qiuyang Dai, Muyuan Tang, Lin Shao, Wen Gou, Zijing Yu, Yanqin Chen, Bei Zheng, Linlin Chen, Conghui Ping, Xiuli Bi, Bin Xiao, Xiaochun Yu, Changliang Liu, Liangyi Chen, Junchao Fan, Xiaoshuai Huang, Yongdeng Zhang

{"title":"Elucidating subcellular architecture and dynamics at isotropic 100-nm resolution with 4Pi-SIM","authors":"Zijing Ouyang, Qian Wang, Xiaoyu Li, Qiuyang Dai, Muyuan Tang, Lin Shao, Wen Gou, Zijing Yu, Yanqin Chen, Bei Zheng, Linlin Chen, Conghui Ping, Xiuli Bi, Bin Xiao, Xiaochun Yu, Changliang Liu, Liangyi Chen, Junchao Fan, Xiaoshuai Huang, Yongdeng Zhang","doi":"10.1038/s41592-024-02515-z","DOIUrl":"10.1038/s41592-024-02515-z","url":null,"abstract":"Three-dimensional structured illumination microscopy (3D-SIM) provides excellent optical sectioning and doubles the resolution in all dimensions compared with wide-field microscopy. However, its much lower axial resolution results in blurred fine details in that direction and overall image distortion. Here we present 4Pi-SIM, a substantial revamp of I5S that synergizes 3D-SIM with interferometric microscopy to achieve isotropic optical resolution through interference in both the illumination and detection wavefronts. We evaluate the performance of 4Pi-SIM by imaging various subcellular structures across different cell types with high fidelity. Furthermore, we demonstrate its capability by conducting time-lapse volumetric imaging over hundreds of time points, achieving a 3D resolution of approximately 100 nm. Additionally, we illustrate its ability to simultaneously image in two colors and capture the rapid interactions between closely positioned organelles in three dimensions. These results underscore the great potential of 4Pi-SIM for elucidating subcellular architecture and revealing dynamic behaviors at the nanoscale. The 4Pi-SIM microscope combines the benefits of structured illumination microscopy with 4Pi geometry for improved axial resolution, offering isotropic, multicolor super-resolution imaging of dynamic processes in living cells.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"335-347"},"PeriodicalIF":36.1,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02515-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142882306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multiplexing strategies to scale up brain organoid modeling 多路复用策略扩大脑类器官模型。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-18 DOI: 10.1038/s41592-024-02556-4

引用次数: 0

Considerations for building and using integrated single-cell atlases 构建和使用集成单细胞图谱的注意事项。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-13 DOI: 10.1038/s41592-024-02532-y

Karin Hrovatin, Lisa Sikkema, Vladimir A. Shitov, Graham Heimberg, Maiia Shulman, Amanda J. Oliver, Michaela F. Mueller, Ignacio L. Ibarra, Hanchen Wang, Ciro Ramírez-Suástegui, Peng He, Anna C. Schaar, Sarah A. Teichmann, Fabian J. Theis, Malte D. Luecken

{"title":"Considerations for building and using integrated single-cell atlases","authors":"Karin Hrovatin, Lisa Sikkema, Vladimir A. Shitov, Graham Heimberg, Maiia Shulman, Amanda J. Oliver, Michaela F. Mueller, Ignacio L. Ibarra, Hanchen Wang, Ciro Ramírez-Suástegui, Peng He, Anna C. Schaar, Sarah A. Teichmann, Fabian J. Theis, Malte D. Luecken","doi":"10.1038/s41592-024-02532-y","DOIUrl":"10.1038/s41592-024-02532-y","url":null,"abstract":"The rapid adoption of single-cell technologies has created an opportunity to build single-cell ‘atlases’ integrating diverse datasets across many laboratories. Such atlases can serve as a reference for analyzing and interpreting current and future data. However, it has become apparent that atlasing approaches differ, and the impact of these differences are often unclear. Here we review the current atlasing literature and present considerations for building and using atlases. Importantly, we find that no one-size-fits-all protocol for atlas building exists, but rather we discuss context-specific considerations and workflows, including atlas conceptualization, data collection, curation and integration, atlas evaluation and atlas sharing. We further highlight the benefits of integrated atlases for analyses of new datasets and deriving biological insights beyond what is possible from individual datasets. Our overview of current practices and associated recommendations will improve the quality of atlases to come, facilitating the shift to a unified, reference-based understanding of single-cell biology. This Review provides a comprehensive and detailed discussion about how to build and use single-cell atlases.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 1","pages":"41-57"},"PeriodicalIF":36.1,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

iFlpMosaics enable the multispectral barcoding and high-throughput comparative analysis of mutant and wild-type cells iFlpMosaics 可对突变型和野生型细胞进行多光谱条形码和高通量比较分析。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-13 DOI: 10.1038/s41592-024-02534-w

Irene Garcia-Gonzalez, Stefano Gambera, Susana F. Rocha, Alvaro Regano, Lourdes Garcia-Ortega, Mariya Lytvyn, Luis Diago-Domingo, Maria S. Sanchez-Muñoz, Aroa Garcia-Cabero, Ivana Zagorac, Wen Luo, Macarena De Andrés-Laguillo, Macarena Fernández-Chacón, Verónica Casquero-Garcia, Federica Francesca Lunella, Carlos Torroja, Fátima Sánchez-Cabo, Rui Benedito

{"title":"iFlpMosaics enable the multispectral barcoding and high-throughput comparative analysis of mutant and wild-type cells","authors":"Irene Garcia-Gonzalez, Stefano Gambera, Susana F. Rocha, Alvaro Regano, Lourdes Garcia-Ortega, Mariya Lytvyn, Luis Diago-Domingo, Maria S. Sanchez-Muñoz, Aroa Garcia-Cabero, Ivana Zagorac, Wen Luo, Macarena De Andrés-Laguillo, Macarena Fernández-Chacón, Verónica Casquero-Garcia, Federica Francesca Lunella, Carlos Torroja, Fátima Sánchez-Cabo, Rui Benedito","doi":"10.1038/s41592-024-02534-w","DOIUrl":"10.1038/s41592-024-02534-w","url":null,"abstract":"To understand gene function, it is necessary to compare cells carrying the mutated target gene with normal cells. In most biomedical studies, the cells being compared are in different mutant and control animals and, therefore, do not experience the same epigenetic changes and tissue microenvironment. The experimental induction of genetic mosaics is essential to determine a gene cell-autonomous function and to model the etiology of diseases caused by somatic mutations. Current technologies used to induce genetic mosaics in mice lack either accuracy, throughput or barcoding diversity. Here we present the iFlpMosaics toolkit comprising a large set of new genetic tools and mouse lines that enable recombinase-dependent ratiometric induction and single-cell clonal tracking of multiple fluorescently labeled wild-type and Cre-mutant cells within the same time window and tissue microenvironment. The labeled cells can be profiled by multispectral imaging or by fluorescence-activated flow cytometry and single-cell RNA sequencing. iFlpMosaics facilitate the induction and analysis of genetic mosaics in any quiescent or progenitor cell, and for any given single or combination of floxed genes, thus enabling a more accurate understanding of how induced genetic mutations affect the biology of single cells during tissue development, homeostasis and disease. iFlpMosaics are a compendium of mouse lines and genetic tools for tissue-agnostic generation and analysis of genetic mosaics.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"323-334"},"PeriodicalIF":36.1,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02534-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Author Correction: Cell Painting: a decade of discovery and innovation in cellular imaging 作者更正：细胞绘画：细胞成像的十年发现和创新。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-12 DOI: 10.1038/s41592-024-02578-y

Srijit Seal, Maria-Anna Trapotsi, Ola Spjuth, Shantanu Singh, Jordi Carreras-Puigvert, Nigel Greene, Andreas Bender, Anne E. Carpenter

引用次数: 0

MouseGoggles: an immersive virtual reality headset for mouse neuroscience and behavior MouseGoggles：用于小鼠神经科学和行为的沉浸式虚拟现实头戴设备。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-12 DOI: 10.1038/s41592-024-02540-y

Matthew Isaacson, Hongyu Chang, Laura Berkowitz, Rick Zirkel, Yusol Park, Danyu Hu, Ian Ellwood, Chris B. Schaffer

{"title":"MouseGoggles: an immersive virtual reality headset for mouse neuroscience and behavior","authors":"Matthew Isaacson, Hongyu Chang, Laura Berkowitz, Rick Zirkel, Yusol Park, Danyu Hu, Ian Ellwood, Chris B. Schaffer","doi":"10.1038/s41592-024-02540-y","DOIUrl":"10.1038/s41592-024-02540-y","url":null,"abstract":"Small-animal virtual reality (VR) systems have become invaluable tools in neuroscience for studying complex behavior during head-fixed neural recording, but they lag behind commercial human VR systems in terms of miniaturization, immersivity and advanced features such as eye tracking. Here we present MouseGoggles, a miniature VR headset for head-fixed mice that delivers independent, binocular visual stimulation over a wide field of view while enabling eye tracking and pupillometry in VR. Neural recordings in the visual cortex validate the quality of image presentation, while hippocampal recordings, associative reward learning and innate fear responses to virtual looming stimuli demonstrate an immersive VR experience. Our open-source system’s simplicity and compact size will enable the broader adoption of VR methods in neuroscience. MouseGoggles is a miniaturized virtual reality (VR) headset for mice that provides an improved immersive experience compared with existing VR equipment. MouseGoggles can also be combined with pupil tracking and has been applied in combination with calcium imaging or electrophysiological recordings.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"380-385"},"PeriodicalIF":36.1,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02540-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142818752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Moculus: an immersive virtual reality system for mice incorporating stereo vision Moculus：结合立体视觉的小鼠沉浸式虚拟现实系统。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-12 DOI: 10.1038/s41592-024-02554-6

Linda Judák, Gergely Dobos, Katalin Ócsai, Eszter Báthory, Huba Szebik, Balázs Tarján, Pál Maák, Zoltán Szadai, István Takács, Balázs Chiovini, Tibor Lőrincz, Áron Szepesi, Botond Roska, Gergely Szalay, Balázs Rózsa

{"title":"Moculus: an immersive virtual reality system for mice incorporating stereo vision","authors":"Linda Judák, Gergely Dobos, Katalin Ócsai, Eszter Báthory, Huba Szebik, Balázs Tarján, Pál Maák, Zoltán Szadai, István Takács, Balázs Chiovini, Tibor Lőrincz, Áron Szepesi, Botond Roska, Gergely Szalay, Balázs Rózsa","doi":"10.1038/s41592-024-02554-6","DOIUrl":"10.1038/s41592-024-02554-6","url":null,"abstract":"Due to technical roadblocks, it is unclear how visual circuits represent multiple features or how behaviorally relevant representations are selected for long-term memory. Here we developed Moculus, a head-mounted virtual reality platform for mice that covers the entire visual field, and allows binocular depth perception and full visual immersion. This controllable environment, with three-dimensional (3D) corridors and 3D objects, in combination with 3D acousto-optical imaging, affords rapid visual learning and the uncovering of circuit substrates in one measurement session. Both the control and reinforcement-associated visual cue coding neuronal assemblies are transiently expanded by reinforcement feedback to near-saturation levels. This increases computational capability and allows competition among assemblies that encode behaviorally relevant information. The coding assemblies form partially orthogonal and overlapping clusters centered around hub cells with higher and earlier ramp-like responses, as well as locally increased functional connectivity. Moculus is a virtual reality headset for mice that allows realistic display of three-dimensional environments. The system improves performance in visual-learning tasks and can be combined with various microscopes to study neural circuitry.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"386-398"},"PeriodicalIF":36.1,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02554-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142818750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0