npj Imaging最新文献_第2页

Robust self-supervised denoising of voltage imaging data using CellMincer 使用CellMincer的电压成像数据鲁棒自监督去噪

npj Imaging Pub Date : 2024-12-04 DOI: 10.1038/s44303-024-00055-x

Brice Wang, Tianle Ma, Theresa Chen, Trinh Nguyen, Ethan Crouse, Stephen J. Fleming, Alison S. Walker, Vera Valakh, Ralda Nehme, Evan W. Miller, Samouil L. Farhi, Mehrtash Babadi

{"title":"Robust self-supervised denoising of voltage imaging data using CellMincer","authors":"Brice Wang, Tianle Ma, Theresa Chen, Trinh Nguyen, Ethan Crouse, Stephen J. Fleming, Alison S. Walker, Vera Valakh, Ralda Nehme, Evan W. Miller, Samouil L. Farhi, Mehrtash Babadi","doi":"10.1038/s44303-024-00055-x","DOIUrl":"10.1038/s44303-024-00055-x","url":null,"abstract":"Voltage imaging is a powerful technique for studying neuronal activity, but its effectiveness is often constrained by low signal-to-noise ratios (SNR). Traditional denoising methods, such as matrix factorization, impose rigid assumptions about noise and signal structures, while existing deep learning approaches fail to fully capture the rapid dynamics and complex dependencies inherent in voltage imaging data. Here, we introduce CellMincer, a novel self-supervised deep learning method specifically developed for denoising voltage imaging datasets. CellMincer operates by masking and predicting sparse pixel sets across short temporal windows and conditions the denoiser on precomputed spatiotemporal auto-correlations to effectively model long-range dependencies without large temporal contexts. We developed and utilized a physics-based simulation framework to generate realistic synthetic datasets, enabling rigorous hyperparameter optimization and ablation studies. This approach highlighted the critical role of conditioning on spatiotemporal auto-correlations, resulting in an additional 3-fold SNR gain. Comprehensive benchmarking on both simulated and real datasets, including those validated with patch-clamp electrophysiology (EP), demonstrates CellMincer’s state-of-the-art performance, with substantial noise reduction across the frequency spectrum, enhanced subthreshold event detection, and high-fidelity recovery of EP signals. CellMincer consistently outperforms existing methods in SNR gain (0.5–2.9 dB) and reduces SNR variability by 17–55%. Incorporating CellMincer into standard workflows significantly improves neuronal segmentation, peak detection, and functional phenotype identification, consistently surpassing current methods in both SNR gain and consistency.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":" ","pages":"1-21"},"PeriodicalIF":0.0,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s44303-024-00055-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142789399","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}

引用次数: 0

Light sheet illumination in single-molecule localization microscopy for imaging of cellular architectures and molecular dynamics 单分子定位显微镜中的光片照明，用于细胞结构和分子动力学成像

npj Imaging Pub Date : 2024-11-21 DOI: 10.1038/s44303-024-00057-9

Siyang Cheng, Yuya Nakatani, Gabriella Gagliano, Nahima Saliba, Anna-Karin Gustavsson

引用次数: 0

Clinical applications of fibroblast activation protein inhibitor positron emission tomography (FAPI-PET) 成纤维细胞活化蛋白抑制剂正电子发射断层扫描（FAPI-PET）的临床应用

npj Imaging Pub Date : 2024-11-13 DOI: 10.1038/s44303-024-00053-z

Yuriko Mori, Emil Novruzov, Dominik Schmitt, Jens Cardinale, Tadashi Watabe, Peter L. Choyke, Abass Alavi, Uwe Haberkorn, Frederik L. Giesel

引用次数: 0

High speed innovations in photoacoustic microscopy 光声显微镜的高速创新

npj Imaging Pub Date : 2024-11-06 DOI: 10.1038/s44303-024-00052-0

Xiaoyi Zhu, Luca Menozzi, Soon-Woo Cho, Junjie Yao

引用次数: 0

Stochastically structured illumination microscopy scan less super resolution imaging 随机结构照明显微镜扫描少超分辨率成像

npj Imaging Pub Date : 2024-11-06 DOI: 10.1038/s44303-024-00047-x

Denzel Fusco, Emmanouil Xypakis, Ylenia Gigante, Lorenza Mautone, Silvia Di Angelantonio, Giorgia Ponsi, Giancarlo Ruocco, Marco Leonetti

{"title":"Stochastically structured illumination microscopy scan less super resolution imaging","authors":"Denzel Fusco, Emmanouil Xypakis, Ylenia Gigante, Lorenza Mautone, Silvia Di Angelantonio, Giorgia Ponsi, Giancarlo Ruocco, Marco Leonetti","doi":"10.1038/s44303-024-00047-x","DOIUrl":"10.1038/s44303-024-00047-x","url":null,"abstract":"In super-resolution, a varying illumination image stack is required. This enriched dataset typically necessitates precise mechanical control and micron-scale optical alignment and repeatability. Here, we introduce a novel methodology for super-resolution microscopy called stochastically structured illumination microscopy (S2IM), which bypasses the need for illumination control exploiting instead the random, uncontrolled movement of the target object. We tested our methodology within the clinically relevant ophthalmoscopic setting, harnessing the inherent saccadic motion of the eye to induce stochastic displacement of the illumination pattern on the retina. We opted to avoid human subjects by utilizing a phantom eye model featuring a retina composed of human induced pluripotent stem cells (iPSC) retinal neurons and replicating the ocular saccadic movements by custom actuators. Our findings demonstrate that S2IM unlocks scan-less super-resolution with a resolution enhancement of 1.91, with promising prospects also beyond ophthalmoscopy applications such as active matter or atmospheric/astronomical observation.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":" ","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s44303-024-00047-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142588291","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}

引用次数: 0

Impact of photobleaching on quantitative, spatio-temporal, super-resolution imaging of mitochondria in live C. elegans larvae 光漂白对线粒体定量、时空、超分辨率活体线粒体成像的影响

npj Imaging Pub Date : 2024-11-06 DOI: 10.1038/s44303-024-00043-1

Segos Ioannis, Van Eeckhoven Jens, Greig Alan, Redd Michael, Thrasivoulou Christopher, Conradt Barbara

{"title":"Impact of photobleaching on quantitative, spatio-temporal, super-resolution imaging of mitochondria in live C. elegans larvae","authors":"Segos Ioannis, Van Eeckhoven Jens, Greig Alan, Redd Michael, Thrasivoulou Christopher, Conradt Barbara","doi":"10.1038/s44303-024-00043-1","DOIUrl":"10.1038/s44303-024-00043-1","url":null,"abstract":"Super-resolution (SR) 3D rendering allows superior quantitative analysis of intracellular structures but has largely been limited to fixed or ex vivo samples. Here we developed a method to perform SR live imaging of mitochondria during post-embryonic development of C. elegans larvae. Our workflow includes the drug-free mechanical immobilisation of animals using polystyrene nanobeads, which has previously not been used for in vivo SR imaging. Based on the alignment of moving objects and global threshold-based image segmentation, our method enables an efficient 3D reconstruction of individual mitochondria. We demonstrate for the first time that the frequency distribution of fluorescence intensities is not affected by photobleaching, and that global thresholding alone enables the quantitative comparison of mitochondria along timeseries. Our composite approach significantly improves the study of biological structures and processes in SR during C. elegans post-embryonic development. Furthermore, the discovery that image segmentation does not require any prior correction against photobleaching, a fundamental problem in fluorescence microscopy, will impact experimental strategies aimed at quantitatively studying the dynamics of organelles and other intracellular compartments in any biological system.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":" ","pages":"1-15"},"PeriodicalIF":0.0,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s44303-024-00043-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142588277","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}

引用次数: 0

Impact of dietary zinc on stimulated zinc secretion MRI in the healthy and malignant mouse prostate 膳食锌对健康和恶性小鼠前列腺锌分泌磁共振成像的影响

npj Imaging Pub Date : 2024-11-06 DOI: 10.1038/s44303-024-00051-1

Veronica Clavijo Jordan, André F. Martins, Erica Dao, Kalotina Geraki, Sara Chirayil, Xiaodong Wen, Pooyan Khalighinejad, Daniel Parrott, Xiaojing Wang, Patricia Gonzalez Pagan, Neil Rofsky, Michael Farquharson, A. Dean Sherry

{"title":"Impact of dietary zinc on stimulated zinc secretion MRI in the healthy and malignant mouse prostate","authors":"Veronica Clavijo Jordan, André F. Martins, Erica Dao, Kalotina Geraki, Sara Chirayil, Xiaodong Wen, Pooyan Khalighinejad, Daniel Parrott, Xiaojing Wang, Patricia Gonzalez Pagan, Neil Rofsky, Michael Farquharson, A. Dean Sherry","doi":"10.1038/s44303-024-00051-1","DOIUrl":"10.1038/s44303-024-00051-1","url":null,"abstract":"Previous studies have shown that the zinc-responsive MRI probe, GdL1, can distinguish healthy versus malignant prostate tissues based upon differences in zinc content and secretion. In this study, mice were fed chow containing low, normal, or high zinc content for 3 weeks before imaging glucose stimulated zinc secretion (GSZS) by MRI. The distribution of zinc in prostate tissue in these three groups was imaged by synchrotron radiation X-ray fluorescence (SR-XRF). A zinc deficiency caused systemic and organ-level dysregulation, weight loss, and altered zinc bioavailability. Zinc efflux from the prostate increased in parallel to dietary zinc in healthy mice but not in TRAMP mice, consistent with a lowered capacity to store dietary zinc in malignant cells. This differential zinc efflux suggests that a dietary supplement of zinc prior to a GSZS study may enhance image contrast between healthy and malignant prostate tissue, thereby improving the accuracy of prostate cancer detection in man.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":" ","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s44303-024-00051-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142588292","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}

引用次数: 0

Deep tissue photoacoustic imaging with light and sound 用光和声音进行深层组织光声成像

npj Imaging Pub Date : 2024-11-06 DOI: 10.1038/s44303-024-00048-w

Luca Menozzi, Junjie Yao

引用次数: 0

Publisher Correction: Magnetic resonance reveals early lipid deposition in murine prediabetes as predictive marker for cardiovascular injury 出版商更正：磁共振发现小鼠糖尿病前期的早期脂质沉积是心血管损伤的预测标志物

npj Imaging Pub Date : 2024-10-11 DOI: 10.1038/s44303-024-00050-2

Katja Heller, Vera Flocke, Tamara Straub, Zhaoping Ding, Tanu Srivastava, Melissa Nowak, Florian Funk, Bodo Levkau, Joachim Schmitt, Maria Grandoch, Ulrich Flögel

引用次数: 0

Label-free live cell recognition and tracking for biological discoveries and translational applications 用于生物发现和转化应用的无标签活细胞识别与追踪技术

npj Imaging Pub Date : 2024-10-07 DOI: 10.1038/s44303-024-00046-y

Biqi Chen, Zi Yin, Billy Wai-Lung Ng, Dan Michelle Wang, Rocky S. Tuan, Ryoma Bise, Dai Fei Elmer Ker

引用次数: 0