Scanning electron microscopy under low-vacuum conditions allows high-resolution imaging of complex cell/tissue architectures in nonconductive specimens. However, the conventional methods for metal staining of biological specimens require harmful uranium compounds, which hampers the applications of electron microscopy. Here, we introduce a uranium-free KMnO4/Pb metal staining protocol that allows multiscale imaging of extensive cell/tissue architectures to intensive subcellular ultrastructures. The obtained image contrast was equivalent to that of Ur/Pb staining and sufficient for ultrastructural observation, showing the fine processes of podocytes in the glomerulus, which were invisible by light microscopy. The stainability in the elastic tissue indicated that the distinct histochemical properties of KMnO4 oxidation led to Pb deposition and BSE signal enhancement superior to Ur staining. Elemental analysis clarified that the determinant of the backscattered electron signal intensity was the amount of Pb deposition enhanced by KMnO4 oxidation. This user-friendly method is anticipated to create a new approach for biomedical electron microscopy.
低真空条件下的扫描电子显微镜可以对不导电标本中复杂的细胞/组织结构进行高分辨率成像。然而，传统的生物标本金属染色方法需要使用有害的铀化合物，这阻碍了电子显微镜的应用。在这里，我们介绍了一种无铀的 KMnO4/Pb 金属染色方案，可对广泛的细胞/组织结构到密集的亚细胞超微结构进行多尺度成像。获得的图像对比度与铀/铅染色相当，足以进行超微结构观察，显示出肾小球中荚膜细胞的精细过程，而光镜下是看不到的。弹性组织中的染色性表明，KMnO4 氧化的独特组织化学特性导致了铅沉积和 BSE 信号增强，其效果优于 Ur 染色。元素分析表明，决定反向散射电子信号强度的因素是 KMnO4 氧化所增强的铅沉积量。这种用户友好型方法有望为生物医学电子显微镜开创一种新方法。
{"title":"KMnO4/Pb staining allows uranium free imaging of tissue architectures in low vacuum scanning electron microscopy","authors":"Akira Sawaguchi, Takeshi Kamimura, Kyoko Kitagawa, Yoko Nagashima, Nobuyasu Takahashi","doi":"10.1038/s44303-024-00045-z","DOIUrl":"10.1038/s44303-024-00045-z","url":null,"abstract":"Scanning electron microscopy under low-vacuum conditions allows high-resolution imaging of complex cell/tissue architectures in nonconductive specimens. However, the conventional methods for metal staining of biological specimens require harmful uranium compounds, which hampers the applications of electron microscopy. Here, we introduce a uranium-free KMnO4/Pb metal staining protocol that allows multiscale imaging of extensive cell/tissue architectures to intensive subcellular ultrastructures. The obtained image contrast was equivalent to that of Ur/Pb staining and sufficient for ultrastructural observation, showing the fine processes of podocytes in the glomerulus, which were invisible by light microscopy. The stainability in the elastic tissue indicated that the distinct histochemical properties of KMnO4 oxidation led to Pb deposition and BSE signal enhancement superior to Ur staining. Elemental analysis clarified that the determinant of the backscattered electron signal intensity was the amount of Pb deposition enhanced by KMnO4 oxidation. This user-friendly method is anticipated to create a new approach for biomedical electron microscopy.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":" ","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s44303-024-00045-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142360072","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}
Pub Date : 2024-09-30DOI: 10.1038/s44303-024-00040-4
Wentao Yu, Yan Zhang, Claudia T. K. Lo, Lei Kang, Terence T. W. Wong
Three-dimensional (3D) high-resolution large-volume imaging has remained a challenge. Translational rapid ultraviolet-excited sectioning tomography (TRUST) achieves rapid and cost-effective whole-organ subcellular imaging through iterative optical scanning and mechanical sectioning. However, the axial resolution is limited by the mechanical sectioning thickness or the UV light penetration depth in tissue. Here, assisted with high-and-low-frequency (HiLo) microscopy (HiLoTRUST), the optical sectioning thickness has been reduced from tens of micrometers to ~5.8 µm. In addition, HiLoTRUST has attained a finer mechanical sectioning thickness (10–15 µm) compared to TRUST (50 µm). For high-content imaging as in TRUST, we employed two additional UV light-emitting diodes (LEDs) specifically for uniform illumination. The full-color imaging ability and improved axial resolution of HiLoTRUST have been validated by two-dimensional (2D)/3D imaging of various mouse organs and human lung cancer specimens. HiLoTRUST offers a cost-effective, full-color, and high-resolution 3D imaging approach, showing its great potential in 3D histology applications.
{"title":"Rapid full-color serial sectioning tomography with speckle illumination and ultraviolet excitation","authors":"Wentao Yu, Yan Zhang, Claudia T. K. Lo, Lei Kang, Terence T. W. Wong","doi":"10.1038/s44303-024-00040-4","DOIUrl":"10.1038/s44303-024-00040-4","url":null,"abstract":"Three-dimensional (3D) high-resolution large-volume imaging has remained a challenge. Translational rapid ultraviolet-excited sectioning tomography (TRUST) achieves rapid and cost-effective whole-organ subcellular imaging through iterative optical scanning and mechanical sectioning. However, the axial resolution is limited by the mechanical sectioning thickness or the UV light penetration depth in tissue. Here, assisted with high-and-low-frequency (HiLo) microscopy (HiLoTRUST), the optical sectioning thickness has been reduced from tens of micrometers to ~5.8 µm. In addition, HiLoTRUST has attained a finer mechanical sectioning thickness (10–15 µm) compared to TRUST (50 µm). For high-content imaging as in TRUST, we employed two additional UV light-emitting diodes (LEDs) specifically for uniform illumination. The full-color imaging ability and improved axial resolution of HiLoTRUST have been validated by two-dimensional (2D)/3D imaging of various mouse organs and human lung cancer specimens. HiLoTRUST offers a cost-effective, full-color, and high-resolution 3D imaging approach, showing its great potential in 3D histology applications.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":" ","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s44303-024-00040-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142329401","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}
Pub Date : 2024-09-23DOI: 10.1038/s44303-024-00041-3
Arora Bharti, Kulkarni Ajinkya, Markus M. Andrea, Ramos-Gomes Fernanda, Bohnenberger Hanibal, Ströbel Philipp, Alves Frauke, Klein Oliver
Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, accentuated by its heterogeneity and complex tumour microenvironment (TME). The role of TME on tumour pathophysiology is pivotal, especially the influence of components of the extracellular matrix (ECM), such as collagen. We introduce a novel multimodal imaging strategy to unravel the complex spatial heterogeneity of CRC by integrating the imaging features from two-photon laser scanning microscopy (2PLSM) and histology with proteomics signatures from matrix-assisted laser desorption ionization-mass spectrometry imaging (MALDI MSI). Our study is the first to correlate the structural coherence of collagen fibres and the nuclei distribution profile of tumour tissue with the peptide signatures, offering insights into the proteomic landscape of CRC within regions of high nuclei distribution (HND), as well as chaotic and organised regions of collagen. We use this approach to distinguish the patient tissues originating from left-sided colorectal cancer (LSCC) and from right-sided colorectal cancer (RSCC). This discriminative signature highlights the role of high nuclei distribution and collagen architecture in tumour progression. Complementary m/z values of several proteins associated to components of ECM, such as plectin, vinculin, vimentin, and myosin, have shown differentially intensity distributions between LSCC and RSCC. Our findings demonstrate the potential of combining structural information with peptide features to identify molecular signatures in different tumour regions and retrieve new insights into CRC pathophysiology.
{"title":"MALDI imaging combined with two-photon microscopy reveals local differences in the heterogeneity of colorectal cancer","authors":"Arora Bharti, Kulkarni Ajinkya, Markus M. Andrea, Ramos-Gomes Fernanda, Bohnenberger Hanibal, Ströbel Philipp, Alves Frauke, Klein Oliver","doi":"10.1038/s44303-024-00041-3","DOIUrl":"10.1038/s44303-024-00041-3","url":null,"abstract":"Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, accentuated by its heterogeneity and complex tumour microenvironment (TME). The role of TME on tumour pathophysiology is pivotal, especially the influence of components of the extracellular matrix (ECM), such as collagen. We introduce a novel multimodal imaging strategy to unravel the complex spatial heterogeneity of CRC by integrating the imaging features from two-photon laser scanning microscopy (2PLSM) and histology with proteomics signatures from matrix-assisted laser desorption ionization-mass spectrometry imaging (MALDI MSI). Our study is the first to correlate the structural coherence of collagen fibres and the nuclei distribution profile of tumour tissue with the peptide signatures, offering insights into the proteomic landscape of CRC within regions of high nuclei distribution (HND), as well as chaotic and organised regions of collagen. We use this approach to distinguish the patient tissues originating from left-sided colorectal cancer (LSCC) and from right-sided colorectal cancer (RSCC). This discriminative signature highlights the role of high nuclei distribution and collagen architecture in tumour progression. Complementary m/z values of several proteins associated to components of ECM, such as plectin, vinculin, vimentin, and myosin, have shown differentially intensity distributions between LSCC and RSCC. Our findings demonstrate the potential of combining structural information with peptide features to identify molecular signatures in different tumour regions and retrieve new insights into CRC pathophysiology.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":" ","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s44303-024-00041-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142276661","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}
Pub Date : 2024-09-23DOI: 10.1038/s44303-024-00044-0
Katja Heller, Vera Flocke, Tamara Straub, Zhaoping Ding, Tanu Srivastava, Melissa Nowak, Florian Funk, Bodo Levkau, Joachim Schmitt, Maria Grandoch, Ulrich Flögel
People with diabetes have an increased cardiovascular risk and a poorer outcome after myocardial infarction (MI). However, the exact underlying mechanisms are still unclear, as is the question of which non-invasive measures could be used to predict the altered risk for the patient at early stages of the disease and adapt personalized treatment. Here, we used a holistic magnetic resonance approach to monitor longitudinally not only the main target heart, but also liver, peripheral/skeletal muscle, bone marrow, and hematopoiesis during disease development and subsequent MI. In prediabetic mice, we found a strong accumulation of lipids in all organs which preceded even a significant whole-body weight gain. Intramyocellular lipids (IMCLs) were most sensitive to reveal in vivo very early alterations in tissue properties during the prediabetic state. Subsequent induction of MI led to a persistent impairment of contractile function in septal/posterior segments of prediabetic hearts which correlated with their lipid load prior MI. At the same time, prediabetic cardiomyocytes exhibited sarcomere function at its limit resulting in overload and lower compensatory contractility of the healthy myocardium after MI. In summary, we identified IMCLs as very early marker in murine prediabetes and together with the cardiac lipid load as predictive for the functional outcome after MI.
{"title":"Magnetic resonance reveals early lipid deposition in murine prediabetes as predictive marker for cardiovascular injury","authors":"Katja Heller, Vera Flocke, Tamara Straub, Zhaoping Ding, Tanu Srivastava, Melissa Nowak, Florian Funk, Bodo Levkau, Joachim Schmitt, Maria Grandoch, Ulrich Flögel","doi":"10.1038/s44303-024-00044-0","DOIUrl":"10.1038/s44303-024-00044-0","url":null,"abstract":"People with diabetes have an increased cardiovascular risk and a poorer outcome after myocardial infarction (MI). However, the exact underlying mechanisms are still unclear, as is the question of which non-invasive measures could be used to predict the altered risk for the patient at early stages of the disease and adapt personalized treatment. Here, we used a holistic magnetic resonance approach to monitor longitudinally not only the main target heart, but also liver, peripheral/skeletal muscle, bone marrow, and hematopoiesis during disease development and subsequent MI. In prediabetic mice, we found a strong accumulation of lipids in all organs which preceded even a significant whole-body weight gain. Intramyocellular lipids (IMCLs) were most sensitive to reveal in vivo very early alterations in tissue properties during the prediabetic state. Subsequent induction of MI led to a persistent impairment of contractile function in septal/posterior segments of prediabetic hearts which correlated with their lipid load prior MI. At the same time, prediabetic cardiomyocytes exhibited sarcomere function at its limit resulting in overload and lower compensatory contractility of the healthy myocardium after MI. In summary, we identified IMCLs as very early marker in murine prediabetes and together with the cardiac lipid load as predictive for the functional outcome after MI.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":" ","pages":"1-16"},"PeriodicalIF":0.0,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s44303-024-00044-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142276646","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}
Pub Date : 2024-09-17DOI: 10.1038/s44303-024-00037-z
Nadia Chaher, Sara Lacerda, Giuseppe Digilio, Sergio Padovan, Ling Gao, Begoña Lavin, Rachele Stefania, Carlos Velasco, Gastão Cruz, Claudia Prieto, René M. Botnar, Alkystis Phinikaridou
Heart failure (HF) affects 64 million people globally with enormous societal and healthcare costs. Myocardial fibrosis, characterised by changes in collagen content drives HF. Despite evidence that collagen type III (COL3) content changes during myocardial fibrosis, in vivo imaging of COL3 has not been achieved. Here, we discovered the first imaging probe that binds to COL3 with high affinity and specificity, by screening candidate peptide-based probes. Characterisation of the probe showed favourable magnetic and biodistribution properties. The probe’s potential for in vivo molecular cardiac magnetic resonance imaging was evaluated in a murine model of myocardial infarction. Using the new probe, we were able to map and quantify, previously undetectable, spatiotemporal changes in COL3 after myocardial infarction and monitor response to treatment. This innovative probe provides a promising tool to non-invasively study the unexplored roles of COL3 in cardiac fibrosis and other cardiovascular conditions marked by changes in COL3.
{"title":"Non-invasive in vivo imaging of changes in Collagen III turnover in myocardial fibrosis","authors":"Nadia Chaher, Sara Lacerda, Giuseppe Digilio, Sergio Padovan, Ling Gao, Begoña Lavin, Rachele Stefania, Carlos Velasco, Gastão Cruz, Claudia Prieto, René M. Botnar, Alkystis Phinikaridou","doi":"10.1038/s44303-024-00037-z","DOIUrl":"10.1038/s44303-024-00037-z","url":null,"abstract":"Heart failure (HF) affects 64 million people globally with enormous societal and healthcare costs. Myocardial fibrosis, characterised by changes in collagen content drives HF. Despite evidence that collagen type III (COL3) content changes during myocardial fibrosis, in vivo imaging of COL3 has not been achieved. Here, we discovered the first imaging probe that binds to COL3 with high affinity and specificity, by screening candidate peptide-based probes. Characterisation of the probe showed favourable magnetic and biodistribution properties. The probe’s potential for in vivo molecular cardiac magnetic resonance imaging was evaluated in a murine model of myocardial infarction. Using the new probe, we were able to map and quantify, previously undetectable, spatiotemporal changes in COL3 after myocardial infarction and monitor response to treatment. This innovative probe provides a promising tool to non-invasively study the unexplored roles of COL3 in cardiac fibrosis and other cardiovascular conditions marked by changes in COL3.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":" ","pages":"1-15"},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s44303-024-00037-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236106","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}
Proton radiotherapy favored over X-ray photon therapy due to its reduced radiation exposure to surrounding healthy tissues, is highly dependent on the accurate positioning of the Bragg peak. Existing methods like PET and prompt gamma imaging to localize Bragg peak face challenges of low precision and high complexity. Here we introduce a 3D protoacoustic imaging with a 2D matrix array of 256 ultrasound transducers compatible with 256 parallel data acquisition channels provides real-time imaging capability (up to 75 frames per second with 10 averages), achieving high precision (5 mm/5% Gamma index shows accuracy better than 95.73%) at depths of tens of centimeters. We have successfully implemented this method in liver treatment with 5 pencil beam scanning and in prostate cancer treatment on a human torso phantom using a clinical proton machine. This demonstrates its capability to accurately identify the Bragg peak in practical clinical scenarios. It paves the way for adaptive radiotherapy with real-time feedback, potentially revolutionizing radiotherapy by enabling closed-loop treatment for improved patient outcomes.
{"title":"Real-time tracking of the Bragg peak during proton therapy via 3D protoacoustic Imaging in a clinical scenario","authors":"Siqi Wang, Gilberto Gonzalez, Leshan Sun, Yifei Xu, Prabodh Pandey, Yong Chen, Shawn (Liangzhong) Xiang","doi":"10.1038/s44303-024-00039-x","DOIUrl":"10.1038/s44303-024-00039-x","url":null,"abstract":"Proton radiotherapy favored over X-ray photon therapy due to its reduced radiation exposure to surrounding healthy tissues, is highly dependent on the accurate positioning of the Bragg peak. Existing methods like PET and prompt gamma imaging to localize Bragg peak face challenges of low precision and high complexity. Here we introduce a 3D protoacoustic imaging with a 2D matrix array of 256 ultrasound transducers compatible with 256 parallel data acquisition channels provides real-time imaging capability (up to 75 frames per second with 10 averages), achieving high precision (5 mm/5% Gamma index shows accuracy better than 95.73%) at depths of tens of centimeters. We have successfully implemented this method in liver treatment with 5 pencil beam scanning and in prostate cancer treatment on a human torso phantom using a clinical proton machine. This demonstrates its capability to accurately identify the Bragg peak in practical clinical scenarios. It paves the way for adaptive radiotherapy with real-time feedback, potentially revolutionizing radiotherapy by enabling closed-loop treatment for improved patient outcomes.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":" ","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s44303-024-00039-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236104","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}
Pub Date : 2024-09-13DOI: 10.1038/s44303-024-00036-0
Ilse J. E. Kouijzer, Nesrin Ghanem-Zoubi
Staphylococcus aureus bacteremia (SAB) is a severe infectious disease with a heterogenous clinical presentation. To diagnose possible metastatic infection and to start early adequate management including antimicrobial treatment and adequate source control as soon as possible, guidelines recommend additional imaging such as [18F]FDG-PET/CT. In this clinical perspective, we describe the current evidence of [18F]FDG-PET/CT in SAB and we share our view on the value of [18F]FDG-PET/CT in specific SAB patients.
金黄色葡萄球菌菌血症（SAB）是一种严重的感染性疾病，临床表现多种多样。为了诊断可能的转移性感染并尽早开始适当的治疗，包括抗菌治疗和充分的病源控制，指南建议进行额外的影像学检查，如[18F]FDG-PET/CT。在本临床视角中，我们描述了[18F]FDG-PET/CT 在 SAB 中的现有证据，并分享了我们对[18F]FDG-PET/CT 在特定 SAB 患者中的价值的看法。
{"title":"The role of [18F]FDG-PET/CT in Staphylococcus aureus bacteremia: A clinical perspective","authors":"Ilse J. E. Kouijzer, Nesrin Ghanem-Zoubi","doi":"10.1038/s44303-024-00036-0","DOIUrl":"10.1038/s44303-024-00036-0","url":null,"abstract":"Staphylococcus aureus bacteremia (SAB) is a severe infectious disease with a heterogenous clinical presentation. To diagnose possible metastatic infection and to start early adequate management including antimicrobial treatment and adequate source control as soon as possible, guidelines recommend additional imaging such as [18F]FDG-PET/CT. In this clinical perspective, we describe the current evidence of [18F]FDG-PET/CT in SAB and we share our view on the value of [18F]FDG-PET/CT in specific SAB patients.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":" ","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s44303-024-00036-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142174351","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}
Pub Date : 2024-09-02DOI: 10.1038/s44303-024-00024-4
Georgeos Hardo, Ruizhe Li, Somenath Bakshi
Time-resolved live-cell imaging using widefield microscopy is instrumental in quantitative microbiology research. It allows researchers to track and measure the size, shape, and content of individual microbial cells over time. However, the small size of microbial cells poses a significant challenge in interpreting image data, as their dimensions approache that of the microscope’s depth of field, and they begin to experience significant diffraction effects. As a result, 2D widefield images of microbial cells contain projected 3D information, blurred by the 3D point spread function. In this study, we employed simulations and targeted experiments to investigate the impact of diffraction and projection on our ability to quantify the size and content of microbial cells from 2D microscopic images. This study points to some new and often unconsidered artefacts resulting from the interplay of projection and diffraction effects, within the context of quantitative microbiology. These artefacts introduce substantial errors and biases in size, fluorescence quantification, and even single-molecule counting, making the elimination of these errors a complex task. Awareness of these artefacts is crucial for designing strategies to accurately interpret micrographs of microbes. To address this, we present new experimental designs and machine learning-based analysis methods that account for these effects, resulting in accurate quantification of microbiological processes.
{"title":"Quantitative microbiology with widefield microscopy: navigating optical artefacts for accurate interpretations","authors":"Georgeos Hardo, Ruizhe Li, Somenath Bakshi","doi":"10.1038/s44303-024-00024-4","DOIUrl":"10.1038/s44303-024-00024-4","url":null,"abstract":"Time-resolved live-cell imaging using widefield microscopy is instrumental in quantitative microbiology research. It allows researchers to track and measure the size, shape, and content of individual microbial cells over time. However, the small size of microbial cells poses a significant challenge in interpreting image data, as their dimensions approache that of the microscope’s depth of field, and they begin to experience significant diffraction effects. As a result, 2D widefield images of microbial cells contain projected 3D information, blurred by the 3D point spread function. In this study, we employed simulations and targeted experiments to investigate the impact of diffraction and projection on our ability to quantify the size and content of microbial cells from 2D microscopic images. This study points to some new and often unconsidered artefacts resulting from the interplay of projection and diffraction effects, within the context of quantitative microbiology. These artefacts introduce substantial errors and biases in size, fluorescence quantification, and even single-molecule counting, making the elimination of these errors a complex task. Awareness of these artefacts is crucial for designing strategies to accurately interpret micrographs of microbes. To address this, we present new experimental designs and machine learning-based analysis methods that account for these effects, resulting in accurate quantification of microbiological processes.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":" ","pages":"1-16"},"PeriodicalIF":0.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s44303-024-00024-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142123432","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}
Focal cortical dysplasia type II (FCD-II) is a prominent cortical development malformation associated with drug-resistant epileptic seizures that leads to lifelong cognitive impairment. Efficient MRI, followed by its analysis (e.g., cortical abnormality distinction, precise localization assistance, etc.) plays a crucial role in the diagnosis and supervision (e.g., presurgery planning and postoperative care) of FCD-II. Involving machine learning techniques particularly, deep-learning (DL) approaches, could enable more effective analysis techniques. We performed a comprehensive study by choosing six different well-known DL models, three image planes (axial, coronal, and sagittal) of two MRI modalities (T1w and FLAIR), demographic characteristics (age and sex) and clinical characteristics (brain hemisphere and lobes) to identify a suitable DL model for analysing FCD-II. The outcomes show that the DenseNet201 model is more suitable because of its superior classification accuracy, high-precision, F1-score, and large area under the receiver operating characteristic (ROC) curve and precision–recall (PR) curve.
{"title":"Focal cortical dysplasia (type II) detection with multi-modal MRI and a deep-learning framework","authors":"Anand Shankar, Manob Jyoti Saikia, Samarendra Dandapat, Shovan Barma","doi":"10.1038/s44303-024-00031-5","DOIUrl":"10.1038/s44303-024-00031-5","url":null,"abstract":"Focal cortical dysplasia type II (FCD-II) is a prominent cortical development malformation associated with drug-resistant epileptic seizures that leads to lifelong cognitive impairment. Efficient MRI, followed by its analysis (e.g., cortical abnormality distinction, precise localization assistance, etc.) plays a crucial role in the diagnosis and supervision (e.g., presurgery planning and postoperative care) of FCD-II. Involving machine learning techniques particularly, deep-learning (DL) approaches, could enable more effective analysis techniques. We performed a comprehensive study by choosing six different well-known DL models, three image planes (axial, coronal, and sagittal) of two MRI modalities (T1w and FLAIR), demographic characteristics (age and sex) and clinical characteristics (brain hemisphere and lobes) to identify a suitable DL model for analysing FCD-II. The outcomes show that the DenseNet201 model is more suitable because of its superior classification accuracy, high-precision, F1-score, and large area under the receiver operating characteristic (ROC) curve and precision–recall (PR) curve.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":" ","pages":"1-18"},"PeriodicalIF":0.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s44303-024-00031-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142123427","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}
Pub Date : 2024-08-21DOI: 10.1038/s44303-024-00032-4
Melissa Chassé, Neil Vasdev
Positron emission tomography (PET) imaging of neurodegenerative disease has historically focused on a small number of established targets. The development of selective PET radiotracers for novel biological targets enables new ways to interrogate the neuropathology of proteinopathies and will advance our understanding of neurodegeneration. This perspective aims to highlight recent PET radiotracers developed for five emerging targets in proteinopathies (i.e., mHTT, BACE1, TDP-43, OGA, and CH24H).
神经退行性疾病的正电子发射断层扫描（PET）成像历来只关注少数几个既定靶点。针对新型生物靶点开发的选择性 PET 放射线racers 可为蛋白质病的神经病理学研究提供新的方法，并将促进我们对神经退行性病变的了解。本视角旨在重点介绍最近针对蛋白病的五个新靶点（即 mHTT、BACE1、TDP-43、OGA 和 CH24H）开发的 PET 放射性racers。
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