Cellular and Molecular Probing of Intact Human Organs

Zhao, Shan, Todorov, Mihail Ivilinov, Cai, Ruiyao, -Maskari, Rami AI, Steinke, Hanno, Kemter, Elisabeth, Mai, Hongcheng, Rong, Zhouyi +15 more·2020·Cell

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  1. Cerebrospinal fluid-contacting neurons are sensory neurons with uniform morphological and region-specific electrophysiological properties in the mouse spinal cord
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  2. Quantitative 3D Imaging of Trypanosoma cruzi-Infected Cells, Dormant Amastigotes, and T Cells in Intact Clarified Organs
    Fernando J. Sánchez-Valdéz, Angel Marcelo Padilla, Juan Manuel Bustamante, Caleb W. D. Hawkins, Rick L. Tarleton · 2022 · Journal of Visualized Experiments
  3. Visualization of 3D Organoids Through the Latest Advancements in Microscopy
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  4. Advances in X-ray neuroimaging: Bridging scales from molecular to organ architectures
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  5. The 14th International Podocyte Conference 2023: from podocyte biology to glomerular medicine
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  7. Smart imaging to empower brain-wide neuroscience at single-cell levels
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  8. Human Developmental Cell Atlas: milestones achieved and the roadmap ahead
    Muzlifah A. Haniffa, Deanne M. Taylor, Sten Linnarsson, Bruce J. Aronow, Gary D. Bader, Pablo G. Cámara, J. Gray Camp, Alain Chédotal, Andrew J. Copp, Heather Etchevers et al. · 2020 · Research Square
  9. Investigating microscopic angioarchitecture in the human visual cortex in 3D with angioMASH tissue clearing and labelling
    Sven Hildebrand, Johannes Franz, Hanna Hoogen, Michael Capalbo, Philipp Bethge, Andreas Herrler, Fritjof Helmchen, Alard F. Roebroeck · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  10. FOCMS: An ultrafast optical clearing method with quantified analysis
    Xiaobin Xu, Yameng Zheng, Xiao Xiao, Zizheng Wang, Jie Lv, Yongjie Wang, Jianmin Zhang, Shumin Duan, Ke Si · 2022 · Frontiers in Physics
  11. Detection of Choroidal Neovascularization Using Optical Tissue Transparency
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  12. Establishment of human Leber’s hereditary optic neuropathy model using iPSC-derived retinal organoids
    Kota Aoshima, Yuya Takagi, Michinori Funato, Yoshiki Kuse, Shinsuke Nakamura, Masamitsu Shimazawa · 2025 · Frontiers in Cellular Neuroscience
  13. Translational pig models for human diseases
    Eckhard Wolf, Asghar Ali, Michaela Blasi, Andreas Blutke, Cornelia A. Deeg, Thomas Fröhlich, Arne Hinrichs, Hristiyan Hristov, Florian Jaudas, Elisabeth Kemter et al. · 2025 · Reproduction Fertility and Development
  14. Chemical dehydration‐induced ultrafast clearing method for human tissues
    Yi Dai, Jianyi Xu, Jie Hao, Zhang Liu, Chengze Lan, Guanghua Xu, Xizhi Meng, Yating Deng, Peng Wan, Kunxing Liu et al. · 2025 · Open Research (University of Surrey)
  15. Rapid 3D Immunolabeling and Light Sheet Microscopy for Quantitative Analysis of Intact Tissues
    Junyu Chen, Zhangfan Ding, Lincoln Biswas, Jessica E. De Angelis, Alexandros Chatzis, Anjali P. Kusumbe · 2026 · Computational and Structural Biotechnology Journal
  16. Revolutionizing the Life Sciences by Developing a Holographic Digital Mannequin
    Bin Cong, Xin‐an Liu, Shiming Zhang, Zhiyu Ni, Liping Wang · 2023 · Engineering
  17. Visualising cancer in 3D: 3‐Dimensional Tissue Imaging for management of cutaneous basal cell carcinoma
    Yingrou Tan, Yuning Zhang, Jackson Liang Yao Li, Hui Yi Chia, Melissa Wee Ping Tan, G. Ebel, Keith Weng Kit Leong, Eiffer Ying Qi Lim, Kylia Kai Ling Chong, Bernett Teck Kwong Lee et al. · 2024 · Experimental Dermatology
  18. Spiner, deep learning-based automated detection of spiral ganglion neurons in intact cochleae
    Yuheng Cai, Greta Leitz-Najarian, Reuben Rosen, Kendall A. Hutson, Adele Moatti, Chen Li, Douglas C. Fitzpatrick, Alon Greenbaum · 2025 · iScience
  19. Innovative affinitätsbasierte Markierungen für die High-End-Mikroskopie
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  20. Detection and Morphological Analysis of Micro-Ruptured Cortical Arteries in Subdural Hematoma: Three-Dimensional Visualization Using the Tissue-Clearing Clear, Unobstructed, Brain/Body Imaging Cocktails and Computational Analysis Method
    Kazuhisa Funayama, Kazuki Tainaka, Akihide Koyama, Rieka Katsuragi-Go, Natsumi Nishikawa-Harada, Ryoko Higuchi, Takashi Aoyama, H Watanabe, Naoya Takahashi, Hisakazu Takatsuka · 2022 · Diagnostics
  21. Hierarchical Random Walker Segmentation for Large Volumetric Biomedical Data.
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  22. IMPASTO: Multiplexed cyclic imaging without signal removal via self-supervised neural unmixing
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  23. Quantitative Multicolored Deep Imaging of Human Bones Reveals a Composite Osteo-Sinusoidal Niche for Mesenchymal Stromal Cells
    Nelson Tsz Long Chu, Ostap A. Dregval, Yu‐Wei Chang, Emil Kryukov, Xin Tian, Xin Liu, Dana Trompet, Misty Shuo Zhang, Lei Li, Zhong Li et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
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  25. FLUID: a fluorescence-friendly lipid-compatible ultrafast clearing method
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  26. An Improved SHANEL Procedure for Clearing and Staining Brain Tissue from Multiple Species
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  27. Multiscale 3D Whole Joint Cellular and Molecular Mapping Reveals Disease‐Specific Neurovascular Plasticity Underlying the Structure‐Pain Relationship
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    Joan J. H. Kim, Shestruma Parajuli, Aman Sinha, Mohammed Mahamdeh, Maaike van den Boomen, Jaume Coll‐Font, Shi Chen, Yiling Fan, Robert A. Eder, Kellie Phipps et al. · 2022 · Frontiers in Cardiovascular Medicine
  34. Prospects of artificial intelligence in regeneration and repair of organs
    Remya Kommeri, Vinoy Thomas · 2023 · Elsevier eBooks
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    Carole Siret, Serge A. van de Pavert · 2023 · Methods in molecular biology
  36. Revealing the MRI‐Contrast in Optically Cleared Brains
    Shimrit Oz, Galit Saar, Shunit Olszakier, Ronit Heinrich, Mykhailo O. Kompanets, Shai Berlin · 2024 · Advanced Science
  37. Towards organism-level systems biology by next-generation genetics and whole-organ cell profiling
    Yoichi Minami, Yufei Yuan, Hiroki R. Ueda · 2021 · Biophysical Reviews
  38. Multimodal Brain Imaging Fusion for the White-Matter Fiber Architecture in the Human Brain
    Ming Song, Zhengyi Yang, Tianzi Jiang · 2022 · Neuroscience Bulletin
  39. Brainbow: Principle, Technique, and Applications
    Kausalya Neelavara Makkithaya, Saina Rath, Sathya Sandilya Garemilla, Sai Sowmya, S. Keerthana, Nirmal Mazumder · 2022 · Springer eBooks
  40. High-Resolution Ex Vivo Tissue Clearing, Lightsheet Imaging, and Data Analysis to Support Macromolecular Drug and Biomarker Distribution in Whole Organs and Tumors
    Niyanta N. Kumar, Petr Hrobař, Martin Vagenknecht, Jindřich Soukup, Peter Bloomingdale, Tomoko Freshwater, Sophia Bardehle, Roman Peter, Nadia Patterson, Ruban Mangadu et al. · 2022 · Microscopy and Microanalysis
  41. Tissue expansion of ‘cleared’ whole brains reduces contrast in ex vivo MRI
    Shimrit Oz, Galit Saar, Shunit Olszakier, Ronit Heinrich, Mykhail Kompanets, Shai Berlin · 2021 · Research Square
  42. COMBINe: Automated Detection and Classification of Neurons and Astrocytes in Tissue Cleared Mouse Brains
    Yuheng Cai, Xuying Zhang, Chen Li, H. Troy Ghashghaei, Alon Greenbaum · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  43. A Light sheet fluorescence microscopy and machine learning-based approach to investigate drug and biomarker distribution in whole organs and tumors
    Niyanta N. Kumar, Petr Hrobař, Martin Vagenknecht, Jindřich Soukup, Nadia Patterson, Peter Bloomingdale, Tomoko Freshwater, Sophia Bardehle, Roman Peter, Ruban Mangadu et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  44. Deep Learning and 3D Imaging Reveal Whole-Body Alterations in Obesity
    Doris Kaltenecker, Izabela Horvath, Rami Al-Maskari, Zeynep Ilgin Kolabas, Ying Chen, Luciano Hoeher, Mihail Ivilinov Todorov, Saketh Kapoor, Mayar Ali, Florian Kofler et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  45. Open-source Photobleacher for Fluorescent Imaging of Large Pigment-Rich Tissues
    Tatsuya C. Murakami, Nick Belenko, Griffin Dennis, Cuidong Wang, Maria Esterlita Siantoputri, Yurie Maeda, Christina Pressl, Nathaniel Heintz · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  46. Rapid immunostaining and high-resolution three-dimensional light-sheet microscopy of intact calcified tissues
    Zhangfan Ding, Yixin Shi, Hanyu Liu, Chunjie Li, J P Chen, Martine Esther Cohen-Solal, Anjali P. Kusumbe · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  47. A safe and reusable imaging chamber compatible with organic solvents
    Martin Colombini, Paweł Pasierbek, Wouter Masselink · 2020 · Microscopy
  48. Une nouvelle méthode de cartographie micrométrique 3D des vaisseaux cérébraux
    Alain Chédotal · 2020 · Comptes Rendus Biologies
  49. [Development in Tissue Clearing Technology and Its Application in Neurodegenerative Diseases].
    Peilin Gu, Jianlei Shen, Ying Jie Zhu, Jiang Li, Lihua Wang · 2021 · PubMed Central
  50. Faculty Opinions recommendation of Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues.
    Eloı́sa Herrera, Augusto Escalante · 2020 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  51. Investigating human neocortical architecture in 3D
    Sven Hildebrand · 2021
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    Ya‐Hui Lin, Li-Wen Wang, Yen‐Hui Chen, Yi-Chieh Chan, Shang‐Hsiu Hu, Sheng‐Yan Wu, Chi‐Shiun Chiang, Guan‐Jie Huang, Shang‐Da Yang, Shi‐Wei Chu et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  53. Imaging the biological microcosmos with a tiny telescope
    2023 · Nature Biotechnology
  54. Diffusion model of delipidation in biological sample clearing
    Jinglu Han, Xin-Yi Liu, Xiaoxiao Hou, Yuejia Zhong, Zhiqiang Chen, Zhenyi Yang, Tianzi Jiang · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  55. Analyse humaner Hirnorganoide vom Millimeter- bis zum Nanometerbreich
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  56. Revealing intact neuronal circuitry in centimeter-sized formalin-fixed paraffin-embedded brain
    Ya‐Hui Lin, Li-Wen Wang, Yen‐Hui Chen, Yi-Chieh Chan, Shang‐Hsiu Hu, Sheng‐Yan Wu, Chi‐Shiun Chiang, Guan‐Jie Huang, Shang‐Da Yang, Shi‐Wei Chu et al. · 2024 · eLife
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  59. Spiner, Deep Learning-Based Automated Detection of Spiral Ganglion Neurons in Intact Cochleae
    Yuheng Cai, Greta Leitz-Najarian, K.A. Hutson, Adele Moatti, Chen Li, Doug Fitzpatrick, Alon Greenbaum · 2024 · SSRN Electronic Journal
  60. Spinal cerebrospinal fluid contacting neurons are a conserved sensory neuronal population along the mouse spinal cord
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