npj Imaging Pub Date : 2025-07-16 DOI: 10.1038/s44303-025-00098-8

Yasmine Kamen, Megan E Doty, Matthew E Ciolkowski, Xhoela Bame, Alicia N Pietramale, Aaron J Schain, Jaime Grutzendler, Robert A Hill

引用次数: 0

FeatureForest: the power of foundation models, the usability of random forests. FeatureForest：基础模型的力量，随机森林的可用性。

npj Imaging Pub Date : 2025-07-08 DOI: 10.1038/s44303-025-00089-9

Mehdi Seifi, Damian Dalle Nogare, Juan Manuel Battagliotti, Vera Galinova, Ananya Kedige Rao, Pierre-Henri Jouneau, Anwai Archit, Constantin Pape, Johan Decelle, Florian Jug, Joran Deschamps

{"title":"FeatureForest: the power of foundation models, the usability of random forests.","authors":"Mehdi Seifi, Damian Dalle Nogare, Juan Manuel Battagliotti, Vera Galinova, Ananya Kedige Rao, Pierre-Henri Jouneau, Anwai Archit, Constantin Pape, Johan Decelle, Florian Jug, Joran Deschamps","doi":"10.1038/s44303-025-00089-9","DOIUrl":"10.1038/s44303-025-00089-9","url":null,"abstract":"Analysis of biological images relies heavily on segmenting the biological objects of interest in the image before performing quantitative analysis. Deep learning (DL) is ubiquitous in such segmentation tasks, but can be cumbersome to apply, as it often requires a large amount of manual labeling to produce ground-truth data, and expert knowledge to train the models. More recently, large foundation models, such as SAM, have shown promising results on scientific images. They, however, require manual prompting for each object or tedious post-processing to selectively segment these objects. Here, we present FeatureForest, a method that leverages the feature embeddings of large foundation models to train a random forest classifier, thereby providing users with a rapid way of semantically segmenting complex images using only a few labeling strokes. We demonstrate the improvement in performance over a variety of datasets and provide an open-source implementation in napari that can be extended to new models.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":"3 1","pages":"32"},"PeriodicalIF":0.0,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12238231/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144593384","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

High contrast fluorescence polarization microscopy through double tagged photoswitchable fluorescent proteins. 高对比荧光偏振显微镜通过双标记的光开关荧光蛋白。

npj Imaging Pub Date : 2025-07-02 DOI: 10.1038/s44303-025-00094-y

Lukas J Münker, Manuel Hohgardt, Andreas Albrecht, Dominik Pfennig, Jan S Tegtmeier, Andreas Holz, Marta Zagrebelsky, Martin Korte, Peter J Walla

{"title":"High contrast fluorescence polarization microscopy through double tagged photoswitchable fluorescent proteins.","authors":"Lukas J Münker, Manuel Hohgardt, Andreas Albrecht, Dominik Pfennig, Jan S Tegtmeier, Andreas Holz, Marta Zagrebelsky, Martin Korte, Peter J Walla","doi":"10.1038/s44303-025-00094-y","DOIUrl":"10.1038/s44303-025-00094-y","url":null,"abstract":"We demonstrate that rigid anchoring of fluorescent proteins through double tagging (FPs) in living cells can significantly enhance the contrast in fluorescence polarization microscopy (FPM) by locking the transition dipole moment orientations to the sample's structures. We applied double tagging of reversibly photoswitchable FPs (dt-rsFPs) to membranes and present a novel camera frame-separated switching pulse scheme that allows effective narrowing of the angle range of excited dt-FP also in living cells (frame-separated excitation polarization angle narrowing, FrExPAN). The principle of rigid anchoring allows specific selection of signals from different structural cell parts with slightly different orientations and is broadly applicable. FrExPAN imaging with dt-rsFPs double-tagged to membranes of living HeLa cells and living hippocampal neurons is demonstrated. We discuss potential implications for orientational contrast imaging as well as super-resolution by polarization demodulation (SPoD) methods.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":"3 1","pages":"31"},"PeriodicalIF":0.0,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12222721/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556387","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

Rethinking deep learning in bioimaging through a data centric lens. 通过以数据为中心的视角重新思考生物成像中的深度学习。

npj Imaging Pub Date : 2025-06-26 DOI: 10.1038/s44303-025-00092-0

Jiajun Cao, Jan Wenzel, Shanghang Zhang, Josephine Lampe, Hongxiao Wang, Jiachen Yao, Zhicheng Zhang, Shuo Zhao, Yu Zhou, Chao Chen, Markus Schwaninger, Jufeng Yang, Danny Z Chen, Jianxu Chen

引用次数: 0

Aldehydic load as an objective imaging biomarker of mild traumatic brain injury. 醛负荷作为轻度外伤性脑损伤的客观成像生物标志物。

npj Imaging Pub Date : 2025-06-26 DOI: 10.1038/s44303-025-00096-w

Alexia Kirby, Cian Ward, Clara S Goulet, Nicholas D Calvert, Ryan Daniel, Joseph Wai-Hin Leung, Ashwin Sharma, Mojmír Suchý, Cassandra Donatelli, Jing Wang, Emily Standen, Adam J Shuhendler

{"title":"Aldehydic load as an objective imaging biomarker of mild traumatic brain injury.","authors":"Alexia Kirby, Cian Ward, Clara S Goulet, Nicholas D Calvert, Ryan Daniel, Joseph Wai-Hin Leung, Ashwin Sharma, Mojmír Suchý, Cassandra Donatelli, Jing Wang, Emily Standen, Adam J Shuhendler","doi":"10.1038/s44303-025-00096-w","DOIUrl":"10.1038/s44303-025-00096-w","url":null,"abstract":"Mild traumatic brain injury (mTBI) is neurological impairment induced by biomechanical forces without structural brain damage, currently without an objective diagnostic tool. Downstream injury stems from oxidative damage leading to the production of neurotoxic aldehydes. A collagen-based 3D corticomimetic in vitro model of concussion was developed, confirming aldehyde production following impact. Total aldehyde levels were mapped in vivo following mTBI using a novel CEST-MRI contrast agent, ProxyNA3, in a new model of closed-head, awake, single-impact concussion in aged and young mice with aldehyde dehydrogenase 2 (ALDH2) deficiency. ProxyNA3-MRI was performed before impact, and on days two- and seven- post-impact. MRI signal enhancement significantly increased at two days post-injury prior to astrocyte activation at seven days post-injury. The data suggest that advanced age and ALDH2 deficiency contribute to increased aldehydic load following mTBI. Overall, ProxyNA3 was capable of mapping concussion-associated aldehydes, supporting its application as an objective diagnostic tool for concussion.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":"3 1","pages":"30"},"PeriodicalIF":0.0,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12202811/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556383","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

Near-infrared fatty acid molecular probe for image-guided surgery of glioblastoma. 近红外脂肪酸分子探针在胶质母细胞瘤影像引导手术中的应用。

npj Imaging Pub Date : 2025-06-23 DOI: 10.1038/s44303-025-00077-z

Meedie Ali, Pavlo Khodakivskyi, Ioannis Ntafoulis, Koen T H van der Kuil, Kranthi M Panth, Arno Roos, Aleksey Yevtodiyenko, Kevin P Francis, Zhenyu Gao, Martine L M Lamfers, Clemens W G M Löwik, Laura Mezzanotte, Elena A Goun

{"title":"Near-infrared fatty acid molecular probe for image-guided surgery of glioblastoma.","authors":"Meedie Ali, Pavlo Khodakivskyi, Ioannis Ntafoulis, Koen T H van der Kuil, Kranthi M Panth, Arno Roos, Aleksey Yevtodiyenko, Kevin P Francis, Zhenyu Gao, Martine L M Lamfers, Clemens W G M Löwik, Laura Mezzanotte, Elena A Goun","doi":"10.1038/s44303-025-00077-z","DOIUrl":"10.1038/s44303-025-00077-z","url":null,"abstract":"Metabolic reprogramming is considered a major driving factor in cancer growth and yet it remains challenging to monitor in vivo uptake of fatty acids, which are essential energy sources for many tumor types. Here, we report the development of a novel, long-chain fatty acid (FA), near-infrared (NIR) imaging reagent (FA-ICG) for real-time, non-invasive imaging of FA absorption in vitro and in vivo. Moreover, we demonstrate the application of the probe in image-guided cancer surgery, where precise assessment of tumor margins is paramount for removal. Specifically, we focus on glioblastoma (GBM), where FA metabolism plays a key role in progression and where there is a significant need for better intraoperative imaging. Here, we successfully demonstrate the application of the probe for NIR in vivo imaging in two different orthotopic models of GBM. In addition, we validate the uptake of the probe in companion dogs with mastocytomas, as these develop cancer with a similar pathology to humans. Our results demonstrate that the probe combines benefits from NIR imaging, such as high sensitivity, low autofluorescence, and deep tissue penetration, with specific tumor metabolism-based targeting and retention. Thus, it represents a promising candidate for a wide range of applications in the fields of metabolic imaging, drug development, and most notably for translation in image-guided surgery.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":"3 1","pages":"28"},"PeriodicalIF":0.0,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12185758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556390","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

Advanced preclinical functional magnetic resonance imaging of the brain. 先进的临床前脑功能磁共振成像。

npj Imaging Pub Date : 2025-06-18 DOI: 10.1038/s44303-025-00085-z

Jan Klohs, Way Cherng Chen, Rikita Araki

引用次数: 0

Copper-mediated radiochemistry: historical impact, current trends, and future possibilities. 铜介导的放射化学：历史影响、当前趋势和未来可能性。

npj Imaging Pub Date : 2025-06-10 eCollection Date: 2025-01-01 DOI: 10.1038/s44303-025-00087-x

Gregory D Bowden, Marius Müller, Matthias M Herth, Melanie S Sanford, Peter J H Scott

引用次数: 0

Multimodal whole slide image processing pipeline for quantitative mapping of tissue architecture and tissue microenvironment. 用于组织结构和组织微环境定量映射的多模态整片图像处理流水线。

npj Imaging Pub Date : 2025-06-10 eCollection Date: 2025-01-01 DOI: 10.1038/s44303-025-00088-w

Maomao Chen, Hongqiang Ma, Xuejiao Sun, Marc Schwartz, Randall E Brand, Jianquan Xu, Dimitrios S Gotsis, Phuong Nguyen, Beverley A Moore, Lori Snyder, Rhonda M Brand, Yang Liu

{"title":"Multimodal whole slide image processing pipeline for quantitative mapping of tissue architecture and tissue microenvironment.","authors":"Maomao Chen, Hongqiang Ma, Xuejiao Sun, Marc Schwartz, Randall E Brand, Jianquan Xu, Dimitrios S Gotsis, Phuong Nguyen, Beverley A Moore, Lori Snyder, Rhonda M Brand, Yang Liu","doi":"10.1038/s44303-025-00088-w","DOIUrl":"10.1038/s44303-025-00088-w","url":null,"abstract":"Multi-modal, multiscale imaging is crucial for quantitative high-content spatial profiling. We present an integrated image processing pipeline for comprehensive tissue analysis that combines quantitative phase microscopy for tissue architecture mapping, hyper-plex fluorescence imaging for immune microenvironment profiling, and whole-slide histopathology. This approach enables detailed morphological mapping of tissue architecture and cell morphology, while simultaneously linking them to the functional states of individual cells across the entire slide. By analyzing tissue biopsies from patients with ulcerative colitis, we demonstrate the potential of this pipeline for quantitative spatial analysis of molecular markers related to mucosal healing. Open-source and compatible with conventional microscopy systems, this pipeline provides a powerful tool for research and clinical applications through its comprehensive integration of quantitative, high-content, and histological imaging modalities.","PeriodicalId":501709,"journal":{"name":"npj Imaging","volume":"3 ","pages":"26"},"PeriodicalIF":0.0,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12151862/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144288095","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

Author Correction: Reactive oxygen species-related oxidative changes are associated with splenic lymphocyte depletion in Ebola virus infection. 作者更正：在埃博拉病毒感染中，活性氧相关的氧化变化与脾淋巴细胞耗竭有关。

npj Imaging Pub Date : 2025-06-02 DOI: 10.1038/s44303-025-00091-1

Venkatesh Mani, Winston T Chu, Hee-Jeong Yang, C Paul Morris, Joseph Laux, Russell Byrum, Kurt Cooper, David X Liu, Hui Wang, Cristal Johnson, Kyra Hadley, John G Bernbaum, Randy Hart, Scott M Anthony, Anthony E Marketon, Rebecca Bernbaum-Cutler, Bapi Pahar, Gabriella Worwa, Jens H Kuhn, Ian Crozier, Claudia Calcagno, Eric Gale

引用次数: 0

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