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Shao W, Shi H, Liu J, Zuo Y, Sun L, Xia T, Chen W, Wan P, Sheng J, Zhu Q, Zhang D. Multi-Instance Multi-Task Learning for Joint Clinical Outcome and Genomic Profile Predictions From the Histopathological Images. IEEE TRANSACTIONS ON MEDICAL IMAGING 2024; 43:2266-2278. [PMID: 38319755 DOI: 10.1109/tmi.2024.3362852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
With the remarkable success of digital histopathology and the deep learning technology, many whole-slide pathological images (WSIs) based deep learning models are designed to help pathologists diagnose human cancers. Recently, rather than predicting categorical variables as in cancer diagnosis, several deep learning studies are also proposed to estimate the continuous variables such as the patients' survival or their transcriptional profile. However, most of the existing studies focus on conducting these predicting tasks separately, which overlooks the useful intrinsic correlation among them that can boost the prediction performance of each individual task. In addition, it is sill challenge to design the WSI-based deep learning models, since a WSI is with huge size but annotated with coarse label. In this study, we propose a general multi-instance multi-task learning framework (HistMIMT) for multi-purpose prediction from WSIs. Specifically, we firstly propose a novel multi-instance learning module (TMICS) considering both common and specific task information across different tasks to generate bag representation for each individual task. Then, a soft-mask based fusion module with channel attention (SFCA) is developed to leverage useful information from the related tasks to help improve the prediction performance on target task. We evaluate our method on three cancer cohorts derived from the Cancer Genome Atlas (TCGA). For each cohort, our multi-purpose prediction tasks range from cancer diagnosis, survival prediction and estimating the transcriptional profile of gene TP53. The experimental results demonstrated that HistMIMT can yield better outcome on all clinical prediction tasks than its competitors.
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2
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Song AH, Williams M, Williamson DFK, Chow SSL, Jaume G, Gao G, Zhang A, Chen B, Baras AS, Serafin R, Colling R, Downes MR, Farré X, Humphrey P, Verrill C, True LD, Parwani AV, Liu JTC, Mahmood F. Analysis of 3D pathology samples using weakly supervised AI. Cell 2024; 187:2502-2520.e17. [PMID: 38729110 DOI: 10.1016/j.cell.2024.03.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/15/2024] [Accepted: 03/25/2024] [Indexed: 05/12/2024]
Abstract
Human tissue, which is inherently three-dimensional (3D), is traditionally examined through standard-of-care histopathology as limited two-dimensional (2D) cross-sections that can insufficiently represent the tissue due to sampling bias. To holistically characterize histomorphology, 3D imaging modalities have been developed, but clinical translation is hampered by complex manual evaluation and lack of computational platforms to distill clinical insights from large, high-resolution datasets. We present TriPath, a deep-learning platform for processing tissue volumes and efficiently predicting clinical outcomes based on 3D morphological features. Recurrence risk-stratification models were trained on prostate cancer specimens imaged with open-top light-sheet microscopy or microcomputed tomography. By comprehensively capturing 3D morphologies, 3D volume-based prognostication achieves superior performance to traditional 2D slice-based approaches, including clinical/histopathological baselines from six certified genitourinary pathologists. Incorporating greater tissue volume improves prognostic performance and mitigates risk prediction variability from sampling bias, further emphasizing the value of capturing larger extents of heterogeneous morphology.
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Affiliation(s)
- Andrew H Song
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mane Williams
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Drew F K Williamson
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah S L Chow
- Department of Mechanical Engineering, Bioengineering, and Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Guillaume Jaume
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gan Gao
- Department of Mechanical Engineering, Bioengineering, and Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Andrew Zhang
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bowen Chen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander S Baras
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert Serafin
- Department of Mechanical Engineering, Bioengineering, and Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Richard Colling
- Nuffield Department of Surgical Sciences, University of Oxford, UK; Department of Cellular Pathology, Oxford University Hospitals NHS Foundations Trust, John Radcliffe Hospital, Oxford, UK
| | - Michelle R Downes
- Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Xavier Farré
- Public Health Agency of Catalonia, Lleida, Spain
| | - Peter Humphrey
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, UK; Department of Cellular Pathology, Oxford University Hospitals NHS Foundations Trust, John Radcliffe Hospital, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lawrence D True
- Department of Laboratory Medicine & Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Anil V Parwani
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Jonathan T C Liu
- Department of Mechanical Engineering, Bioengineering, and Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA.
| | - Faisal Mahmood
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA.
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Park WY, Yun J, Shin J, Oh BH, Yoon G, Hong SM, Kim KH. Open-top Bessel beam two-photon light sheet microscopy for three-dimensional pathology. eLife 2024; 12:RP92614. [PMID: 38488831 PMCID: PMC10942781 DOI: 10.7554/elife.92614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Abstract
Nondestructive pathology based on three-dimensional (3D) optical microscopy holds promise as a complement to traditional destructive hematoxylin and eosin (H&E) stained slide-based pathology by providing cellular information in high throughput manner. However, conventional techniques provided superficial information only due to shallow imaging depths. Herein, we developed open-top two-photon light sheet microscopy (OT-TP-LSM) for intraoperative 3D pathology. An extended depth of field two-photon excitation light sheet was generated by scanning a nondiffractive Bessel beam, and selective planar imaging was conducted with cameras at 400 frames/s max during the lateral translation of tissue specimens. Intrinsic second harmonic generation was collected for additional extracellular matrix (ECM) visualization. OT-TP-LSM was tested in various human cancer specimens including skin, pancreas, and prostate. High imaging depths were achieved owing to long excitation wavelengths and long wavelength fluorophores. 3D visualization of both cells and ECM enhanced the ability of cancer detection. Furthermore, an unsupervised deep learning network was employed for the style transfer of OT-TP-LSM images to virtual H&E images. The virtual H&E images exhibited comparable histological characteristics to real ones. OT-TP-LSM may have the potential for histopathological examination in surgical and biopsy applications by rapidly providing 3D information.
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Affiliation(s)
- Won Yeong Park
- Department of Mechanical Engineering, Pohang University of Science and TechnologyPohangRepublic of Korea
| | - Jieun Yun
- Department of Mechanical Engineering, Pohang University of Science and TechnologyPohangRepublic of Korea
| | - Jinho Shin
- Department of Medicine, University of Ulsan College of Medicine, SeoulSeoulRepublic of Korea
| | - Byung Ho Oh
- Department of Dermatology, College of Medicine, Yonsei UniversitySeoulRepublic of Korea
| | - Gilsuk Yoon
- Department of Pathology, School of Medicine, Kyungpook National UniversityDaeguRepublic of Korea
| | - Seung-Mo Hong
- Department of Pathology, Asan Medical Center, University of Ulsan College of MedicineSeoulRepublic of Korea
| | - Ki Hean Kim
- Department of Mechanical Engineering, Pohang University of Science and TechnologyPohangRepublic of Korea
- Medical Science and Engineering Program, School of Convergence Science and Technology, Pohang University of Science and TechnologyPohangRepublic of Korea
- Institute for Convergence Research and Education in Advanced Technology, Yonsei UniversitySeoulRepublic of Korea
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Fan Y, Liu S, Gao E, Guo R, Dong G, Li Y, Gao T, Tang X, Liao H. The LMIT: Light-mediated minimally-invasive theranostics in oncology. Theranostics 2024; 14:341-362. [PMID: 38164160 PMCID: PMC10750201 DOI: 10.7150/thno.87783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/18/2023] [Indexed: 01/03/2024] Open
Abstract
Minimally-invasive diagnosis and therapy have gradually become the trend and research hotspot of current medical applications. The integration of intraoperative diagnosis and treatment is a development important direction for real-time detection, minimally-invasive diagnosis and therapy to reduce mortality and improve the quality of life of patients, so called minimally-invasive theranostics (MIT). Light is an important theranostic tool for the treatment of cancerous tissues. Light-mediated minimally-invasive theranostics (LMIT) is a novel evolutionary technology that integrates diagnosis and therapeutics for the less invasive treatment of diseased tissues. Intelligent theranostics would promote precision surgery based on the optical characterization of cancerous tissues. Furthermore, MIT also requires the assistance of smart medical devices or robots. And, optical multimodality lay a solid foundation for intelligent MIT. In this review, we summarize the important state-of-the-arts of optical MIT or LMIT in oncology. Multimodal optical image-guided intelligent treatment is another focus. Intraoperative imaging and real-time analysis-guided optical treatment are also systemically discussed. Finally, the potential challenges and future perspectives of intelligent optical MIT are discussed.
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Affiliation(s)
- Yingwei Fan
- School of Medical Technology, Beijing Institute of Technology, Beijing, China, 100081
| | - Shuai Liu
- School of Medical Technology, Beijing Institute of Technology, Beijing, China, 100081
| | - Enze Gao
- School of Medical Technology, Beijing Institute of Technology, Beijing, China, 100081
| | - Rui Guo
- School of Medical Technology, Beijing Institute of Technology, Beijing, China, 100081
| | - Guozhao Dong
- School of Medical Technology, Beijing Institute of Technology, Beijing, China, 100081
| | - Yangxi Li
- Dept. of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China, 100084
| | - Tianxin Gao
- School of Medical Technology, Beijing Institute of Technology, Beijing, China, 100081
| | - Xiaoying Tang
- School of Medical Technology, Beijing Institute of Technology, Beijing, China, 100081
| | - Hongen Liao
- Dept. of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China, 100084
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5
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McKenzie AT, Nnadi O, Slagell KD, Thorn EL, Farrell K, Crary JF. Fluid preservation in brain banking: a review. FREE NEUROPATHOLOGY 2024; 5:5-10. [PMID: 38690035 PMCID: PMC11058410 DOI: 10.17879/freeneuropathology-2024-5373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/29/2024] [Indexed: 05/02/2024]
Abstract
Fluid preservation is nearly universally used in brain banking to store fixed tissue specimens for future research applications. However, the effects of long-term immersion on neural circuitry and biomolecules are not well characterized. As a result, there is a need to synthesize studies investigating fluid preservation of brain tissue. We searched PubMed and other databases to identify studies measuring the effects of fluid preservation in nervous system tissue. We categorized studies based on the fluid preservative used: formaldehyde solutions, buffer solutions, alcohol solutions, storage after tissue clearing, and cryoprotectant solutions. We identified 91 studies containing 197 independent observations of the effects of long-term storage on cellular morphology. Most studies did not report any significant alterations due to long-term storage. When present, the most frequent alteration was decreased antigenicity, commonly attributed to progressive crosslinking by aldehydes that renders biomolecules increasingly inaccessible over time. To build a mechanistic understanding, we discuss biochemical aspects of long-term fluid preservation. A subset of lipids appears to be chemical altered or extracted over time due to incomplete retention in the crosslinked gel. Alternative storage fluids mitigate the problem of antigen masking but have not been extensively characterized and may have other downsides. We also compare fluid preservation to cryopreservation, paraffin embedding, and resin embedding. Overall, existing evidence suggests that fluid preservation provides maintenance of neural architecture for decades, including precise structural details. However, to avoid the well-established problem of overfixation caused by storage in high concentration formaldehyde solutions, fluid preservation procedures can use an initial fixation step followed by an alternative long-term storage fluid. Further research is warranted on optimizing protocols and characterizing the generalizability of the storage artifacts that have been identified.
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Affiliation(s)
| | - Oge Nnadi
- Brain Preservation Foundation, Ashburn, Virginia, USA
| | - Kat D. Slagell
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emma L. Thorn
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kurt Farrell
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John F. Crary
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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6
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Pal R, Lwin TM, Krishnamoorthy M, Collins HR, Chan CD, Prilutskiy A, Nasrallah MP, Dijkhuis TH, Shukla S, Kendall AL, Marshall MS, Carp SA, Hung YP, Shih AR, Martinez-Lage M, Zukerberg L, Sadow PM, Faquin WC, Nahed BV, Feng AL, Emerick KS, Mieog JSD, Vahrmeijer AL, Rajasekaran K, Lee JYK, Rankin KS, Lozano-Calderon S, Varvares MA, Tanabe KK, Kumar ATN. Fluorescence lifetime of injected indocyanine green as a universal marker of solid tumours in patients. Nat Biomed Eng 2023; 7:1649-1666. [PMID: 37845517 DOI: 10.1038/s41551-023-01105-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 09/10/2023] [Indexed: 10/18/2023]
Abstract
The surgical resection of solid tumours can be enhanced by fluorescence-guided imaging. However, variable tumour uptake and incomplete clearance of fluorescent dyes reduces the accuracy of distinguishing tumour from normal tissue via conventional fluorescence intensity-based imaging. Here we show that, after systemic injection of the near-infrared dye indocyanine green in patients with various types of solid tumour, the fluorescence lifetime (FLT) of tumour tissue is longer than the FLT of non-cancerous tissue. This tumour-specific shift in FLT can be used to distinguish tumours from normal tissue with an accuracy of over 97% across tumour types, and can be visualized at the cellular level using microscopy and in larger specimens through wide-field imaging. Unlike fluorescence intensity, which depends on imaging-system parameters, tissue depth and the amount of dye taken up by tumours, FLT is a photophysical property that is largely independent of these factors. FLT imaging with indocyanine green may improve the accuracy of cancer surgeries.
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Affiliation(s)
- Rahul Pal
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Thinzar M Lwin
- Department of Surgical Oncology, City of Hope Hospital, Duarte, CA, USA
| | - Murali Krishnamoorthy
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Hannah R Collins
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Corey D Chan
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Andrey Prilutskiy
- Department of Pathology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - MacLean P Nasrallah
- Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Tom H Dijkhuis
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Shriya Shukla
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Amy L Kendall
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Michael S Marshall
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Stefan A Carp
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Yin P Hung
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Angela R Shih
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Maria Martinez-Lage
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lawrence Zukerberg
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter M Sadow
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Otolaryngology and Head and Neck Surgery, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - William C Faquin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Otolaryngology and Head and Neck Surgery, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Brian V Nahed
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Allen L Feng
- Department of Otolaryngology and Head and Neck Surgery, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Kevin S Emerick
- Department of Otolaryngology and Head and Neck Surgery, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - J Sven D Mieog
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Karthik Rajasekaran
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - John Y K Lee
- Department of Neurosurgery, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth S Rankin
- The North of England Bone and Soft Tissue Tumour Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Santiago Lozano-Calderon
- Department of Orthopedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark A Varvares
- Department of Otolaryngology and Head and Neck Surgery, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Kenneth K Tanabe
- Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Anand T N Kumar
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA.
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7
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Hou H, Mitbander R, Tang Y, Azimuddin A, Carns J, Schwarz RA, Richards-Kortum RR. Optical imaging technologies for in vivo cancer detection in low-resource settings. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2023; 28:100495. [PMID: 38406798 PMCID: PMC10883072 DOI: 10.1016/j.cobme.2023.100495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Cancer continues to affect underserved populations disproportionately. Novel optical imaging technologies, which can provide rapid, non-invasive, and accurate cancer detection at the point of care, have great potential to improve global cancer care. This article reviews the recent technical innovations and clinical translation of low-cost optical imaging technologies, highlighting the advances in both hardware and software, especially the integration of artificial intelligence, to improve in vivo cancer detection in low-resource settings. Additionally, this article provides an overview of existing challenges and future perspectives of adapting optical imaging technologies into clinical practice, which can potentially contribute to novel insights and programs that effectively improve cancer detection in low-resource settings.
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Affiliation(s)
- Huayu Hou
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Ruchika Mitbander
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Yubo Tang
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Ahad Azimuddin
- School of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Jennifer Carns
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Richard A Schwarz
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
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8
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Park S, Na M, Chang S, Kim KH. High-resolution open-top axially swept light sheet microscopy. BMC Biol 2023; 21:248. [PMID: 37940973 PMCID: PMC10634022 DOI: 10.1186/s12915-023-01747-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Open-top light-sheet microscopy (OT-LSM) is a specialized microscopic technique for the high-throughput cellular imaging of optically cleared, large-sized specimens, such as the brain. Despite the development of various OT-LSM techniques, achieving submicron resolution in all dimensions remains. RESULTS We developed a high-resolution open-top axially swept LSM (HR-OTAS-LSM) for high-throughput and high-resolution imaging in all dimensions. High axial and lateral resolutions were achieved by using an aberration-corrected axially swept excitation light sheet in the illumination arm and a high numerical aperture (NA) immersion objective lens in the imaging arm, respectively. The high-resolution, high-throughput visualization of neuronal networks in mouse brain and retina specimens validated the performance of HR-OTAS-LSM. CONCLUSIONS The proposed HR-OTAS-LSM method represents a significant advancement in the high-resolution mapping of cellular networks in biological systems such as the brain and retina.
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Affiliation(s)
- Soohyun Park
- Department of Mechanical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Myeongsu Na
- Department of Research and Development Center, Crayon Technologies, 19 Sanmaru-ro, Guri, Gyeonggi-do, 11901, Republic of Korea
| | - Sunghoe Chang
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Ki Hean Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea.
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9
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Alieva M, Wezenaar AKL, Wehrens EJ, Rios AC. Bridging live-cell imaging and next-generation cancer treatment. Nat Rev Cancer 2023; 23:731-745. [PMID: 37704740 DOI: 10.1038/s41568-023-00610-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/25/2023] [Indexed: 09/15/2023]
Abstract
By providing spatial, molecular and morphological data over time, live-cell imaging can provide a deeper understanding of the cellular and signalling events that determine cancer response to treatment. Understanding this dynamic response has the potential to enhance clinical outcome by identifying biomarkers or actionable targets to improve therapeutic efficacy. Here, we review recent applications of live-cell imaging for uncovering both tumour heterogeneity in treatment response and the mode of action of cancer-targeting drugs. Given the increasing uses of T cell therapies, we discuss the unique opportunity of time-lapse imaging for capturing the interactivity and motility of immunotherapies. Although traditionally limited in the number of molecular features captured, novel developments in multidimensional imaging and multi-omics data integration offer strategies to connect single-cell dynamics to molecular phenotypes. We review the effect of these recent technological advances on our understanding of the cellular dynamics of tumour targeting and discuss their implication for next-generation precision medicine.
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Affiliation(s)
- Maria Alieva
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Instituto de Investigaciones Biomedicas Sols-Morreale (IIBM), CSIC-UAM, Madrid, Spain
| | - Amber K L Wezenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Ellen J Wehrens
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
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10
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Martell MT, Haven NJM, Cikaluk BD, Restall BS, McAlister EA, Mittal R, Adam BA, Giannakopoulos N, Peiris L, Silverman S, Deschenes J, Li X, Zemp RJ. Deep learning-enabled realistic virtual histology with ultraviolet photoacoustic remote sensing microscopy. Nat Commun 2023; 14:5967. [PMID: 37749108 PMCID: PMC10519961 DOI: 10.1038/s41467-023-41574-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/11/2023] [Indexed: 09/27/2023] Open
Abstract
The goal of oncologic surgeries is complete tumor resection, yet positive margins are frequently found postoperatively using gold standard H&E-stained histology methods. Frozen section analysis is sometimes performed for rapid intraoperative margin evaluation, albeit with known inaccuracies. Here, we introduce a label-free histological imaging method based on an ultraviolet photoacoustic remote sensing and scattering microscope, combined with unsupervised deep learning using a cycle-consistent generative adversarial network for realistic virtual staining. Unstained tissues are scanned at rates of up to 7 mins/cm2, at resolution equivalent to 400x digital histopathology. Quantitative validation suggests strong concordance with conventional histology in benign and malignant prostate and breast tissues. In diagnostic utility studies we demonstrate a mean sensitivity and specificity of 0.96 and 0.91 in breast specimens, and respectively 0.87 and 0.94 in prostate specimens. We also find virtual stain quality is preferred (P = 0.03) compared to frozen section analysis in a blinded survey of pathologists.
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Affiliation(s)
- Matthew T Martell
- Department of Electrical and Computer Engineering, University of Alberta, 116 Street & 85 Avenue, Edmonton, AB, T6G 2R3, Canada
| | - Nathaniel J M Haven
- Department of Electrical and Computer Engineering, University of Alberta, 116 Street & 85 Avenue, Edmonton, AB, T6G 2R3, Canada
| | - Brendyn D Cikaluk
- Department of Electrical and Computer Engineering, University of Alberta, 116 Street & 85 Avenue, Edmonton, AB, T6G 2R3, Canada
| | - Brendon S Restall
- Department of Electrical and Computer Engineering, University of Alberta, 116 Street & 85 Avenue, Edmonton, AB, T6G 2R3, Canada
| | - Ewan A McAlister
- Department of Electrical and Computer Engineering, University of Alberta, 116 Street & 85 Avenue, Edmonton, AB, T6G 2R3, Canada
| | - Rohan Mittal
- Department of Laboratory Medicine and Pathology, University of Alberta, 11405 87 Avenue NW, Edmonton, AB, T6G 1C9, Canada
| | - Benjamin A Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, 11405 87 Avenue NW, Edmonton, AB, T6G 1C9, Canada
| | - Nadia Giannakopoulos
- Department of Laboratory Medicine and Pathology, University of Alberta, 11405 87 Avenue NW, Edmonton, AB, T6G 1C9, Canada
| | - Lashan Peiris
- Department of Surgery, University of Alberta, 8440 - 112 Street, Edmonton, AB, T6G 2B7, Canada
| | - Sveta Silverman
- Department of Laboratory Medicine and Pathology, University of Alberta, 11405 87 Avenue NW, Edmonton, AB, T6G 1C9, Canada
| | - Jean Deschenes
- Department of Laboratory Medicine and Pathology, University of Alberta, 11405 87 Avenue NW, Edmonton, AB, T6G 1C9, Canada
| | - Xingyu Li
- Department of Electrical and Computer Engineering, University of Alberta, 116 Street & 85 Avenue, Edmonton, AB, T6G 2R3, Canada
| | - Roger J Zemp
- Department of Electrical and Computer Engineering, University of Alberta, 116 Street & 85 Avenue, Edmonton, AB, T6G 2R3, Canada.
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11
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Song AH, Williams M, Williamson DFK, Jaume G, Zhang A, Chen B, Serafin R, Liu JTC, Baras A, Parwani AV, Mahmood F. Weakly Supervised AI for Efficient Analysis of 3D Pathology Samples. ARXIV 2023:arXiv:2307.14907v1. [PMID: 37547660 PMCID: PMC10402184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Human tissue consists of complex structures that display a diversity of morphologies, forming a tissue microenvironment that is, by nature, three-dimensional (3D). However, the current standard-of-care involves slicing 3D tissue specimens into two-dimensional (2D) sections and selecting a few for microscopic evaluation1,2, with concomitant risks of sampling bias and misdiagnosis3-6. To this end, there have been intense efforts to capture 3D tissue morphology and transition to 3D pathology, with the development of multiple high-resolution 3D imaging modalities7-18. However, these tools have had little translation to clinical practice as manual evaluation of such large data by pathologists is impractical and there is a lack of computational platforms that can efficiently process the 3D images and provide patient-level clinical insights. Here we present Modality-Agnostic Multiple instance learning for volumetric Block Analysis (MAMBA), a deep-learning-based platform for processing 3D tissue images from diverse imaging modalities and predicting patient outcomes. Archived prostate cancer specimens were imaged with open-top light-sheet microscopy12-14 or microcomputed tomography15,16 and the resulting 3D datasets were used to train risk-stratification networks based on 5-year biochemical recurrence outcomes via MAMBA. With the 3D block-based approach, MAMBA achieves an area under the receiver operating characteristic curve (AUC) of 0.86 and 0.74, superior to 2D traditional single-slice-based prognostication (AUC of 0.79 and 0.57), suggesting superior prognostication with 3D morphological features. Further analyses reveal that the incorporation of greater tissue volume improves prognostic performance and mitigates risk prediction variability from sampling bias, suggesting that there is value in capturing larger extents of spatially heterogeneous 3D morphology. With the rapid growth and adoption of 3D spatial biology and pathology techniques by researchers and clinicians, MAMBA provides a general and efficient framework for 3D weakly supervised learning for clinical decision support and can help to reveal novel 3D morphological biomarkers for prognosis and therapeutic response.
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Affiliation(s)
- Andrew H. Song
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mane Williams
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Drew F. K. Williamson
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Guillaume Jaume
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andrew Zhang
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bowen Chen
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert Serafin
- Department of Mechanical Engineering, Bioengineering, and Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Jonathan T. C. Liu
- Department of Mechanical Engineering, Bioengineering, and Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Alex Baras
- Department of Pathology, Johns Hopkins Hospital, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Anil V. Parwani
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Faisal Mahmood
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
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12
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Peterson T, Mann S, Sun BL, Peng L, Cai H, Liang R. Motionless volumetric structured light sheet microscopy. BIOMEDICAL OPTICS EXPRESS 2023; 14:2209-2224. [PMID: 37206125 PMCID: PMC10191636 DOI: 10.1364/boe.489280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 05/21/2023]
Abstract
To meet the increasing need for low-cost, compact imaging technology with cellular resolution, we have developed a microLED-based structured light sheet microscope for three-dimensional ex vivo and in vivo imaging of biological tissue in multiple modalities. All the illumination structure is generated directly at the microLED panel-which serves as the source-so light sheet scanning and modulation is completely digital, yielding a system that is simpler and less prone to error than previously reported methods. Volumetric images with optical sectioning are thus achieved in an inexpensive, compact form factor without any moving parts. We demonstrate the unique properties and general applicability of our technique by ex vivo imaging of porcine and murine tissue from the gastrointestinal tract, kidney, and brain.
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Affiliation(s)
- Tyler Peterson
- Wyant College of Optical Sciences,
The University of Arizona, Tucson, Arizona 85721, USA
| | - Shivani Mann
- Department of Neuroscience, The University of Arizona, Tucson, Arizona 85721, USA
| | - Belinda L. Sun
- Department of Pathology, College of Medicine, The University of Arizona, Tucson, Arizona 85721, USA
| | - Leilei Peng
- Wyant College of Optical Sciences,
The University of Arizona, Tucson, Arizona 85721, USA
| | - Haijiang Cai
- Department of Neuroscience, The University of Arizona, Tucson, Arizona 85721, USA
| | - Rongguang Liang
- Wyant College of Optical Sciences,
The University of Arizona, Tucson, Arizona 85721, USA
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13
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Zhou KC, Harfouche M, Cooke CL, Park J, Konda PC, Kreiss L, Kim K, Jönsson J, Doman T, Reamey P, Saliu V, Cook CB, Zheng M, Bechtel JP, Bègue A, McCarroll M, Bagwell J, Horstmeyer G, Bagnat M, Horstmeyer R. Parallelized computational 3D video microscopy of freely moving organisms at multiple gigapixels per second. NATURE PHOTONICS 2023; 17:442-450. [PMID: 37808252 PMCID: PMC10552607 DOI: 10.1038/s41566-023-01171-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/03/2023] [Indexed: 10/10/2023]
Abstract
Wide field of view microscopy that can resolve 3D information at high speed and spatial resolution is highly desirable for studying the behaviour of freely moving model organisms. However, it is challenging to design an optical instrument that optimises all these properties simultaneously. Existing techniques typically require the acquisition of sequential image snapshots to observe large areas or measure 3D information, thus compromising on speed and throughput. Here, we present 3D-RAPID, a computational microscope based on a synchronized array of 54 cameras that can capture high-speed 3D topographic videos over an area of 135 cm2, achieving up to 230 frames per second at spatiotemporal throughputs exceeding 5 gigapixels per second. 3D-RAPID employs a 3D reconstruction algorithm that, for each synchronized snapshot, fuses all 54 images into a composite that includes a co-registered 3D height map. The self-supervised 3D reconstruction algorithm trains a neural network to map raw photometric images to 3D topography using stereo overlap redundancy and ray-propagation physics as the only supervision mechanism. The resulting reconstruction process is thus robust to generalization errors and scales to arbitrarily long videos from arbitrarily sized camera arrays. We demonstrate the broad applicability of 3D-RAPID with collections of several freely behaving organisms, including ants, fruit flies, and zebrafish larvae.
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Affiliation(s)
- Kevin C. Zhou
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
- Current affiliation: Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | - Mark Harfouche
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
| | - Colin L. Cooke
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Jaehee Park
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
| | - Pavan C. Konda
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Lucas Kreiss
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Kanghyun Kim
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Joakim Jönsson
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Thomas Doman
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
| | - Paul Reamey
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
| | - Veton Saliu
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
| | - Clare B. Cook
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
| | - Maxwell Zheng
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
| | | | - Aurélien Bègue
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
| | - Matthew McCarroll
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Jennifer Bagwell
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | | | - Michel Bagnat
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | - Roarke Horstmeyer
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
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14
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Ngo TB, DeStefano S, Liu J, Su Y, Shroff H, Vishwasrao HD, Sadtler K. Label-free cleared tissue microscopy and machine learning for 3D histopathology of biomaterial implants. J Biomed Mater Res A 2023; 111:840-850. [PMID: 36861434 DOI: 10.1002/jbm.a.37515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/18/2023] [Accepted: 02/08/2023] [Indexed: 03/03/2023]
Abstract
Tissue clearing of whole intact organs has enhanced imaging by enabling the exploration of tissue structure at a subcellular level in three-dimensional space. Although clearing and imaging of the whole organ have been used to study tissue biology, the microenvironment in which cells evolve to adapt to biomaterial implants or allografts in the body is poorly understood. Obtaining high-resolution information from complex cell-biomaterial interactions with volumetric landscapes represents a key challenge in the fields of biomaterials and regenerative medicine. To provide a new approach to examine how tissue responds to biomaterial implants, we apply cleared tissue light-sheet microscopy and three-dimensional reconstruction to utilize the wealth of autofluorescence information for visualizing and contrasting anatomical structures. This study demonstrates the adaptability of the clearing and imaging technique to provide sub-cellular resolution (0.6 μm isotropic) 3D maps of various tissue types, using samples from fully intact peritoneal organs to volumetric muscle loss injury specimens. Specifically, in the volumetric muscle loss injury model, we provide 3D visualization of the implanted extracellular matrix biomaterial in the wound bed of the quadricep muscle groups and further apply computational-driven image classification to analyze the autofluorescence spectrum at multiple emission wavelengths to categorize tissue types at the injured site interacting with the biomaterial scaffolds.
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Affiliation(s)
- Tran B Ngo
- Section on Immunoengineering, Bioengineering and Technology Acceleration Center, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Sabrina DeStefano
- Section on Immunoengineering, Bioengineering and Technology Acceleration Center, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Jiamin Liu
- Advanced Imaging and Microscopy Resource, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Yijun Su
- Advanced Imaging and Microscopy Resource, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Hari Shroff
- Advanced Imaging and Microscopy Resource, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Harshad D Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Kaitlyn Sadtler
- Section on Immunoengineering, Bioengineering and Technology Acceleration Center, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
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15
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Wang T, Chen Y, Wang B, Wu M. Recent progress of second near-infrared (NIR-II) fluorescence microscopy in bioimaging. Front Physiol 2023; 14:1126805. [PMID: 36895633 PMCID: PMC9990761 DOI: 10.3389/fphys.2023.1126805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
Visualizing biological tissues in vivo at a cellular or subcellular resolution to explore molecular signaling and cell behaviors is a crucial direction for research into biological processes. In vivo imaging can provide quantitative and dynamic visualization/mapping in biology and immunology. New microscopy techniques combined with near-infrared region fluorophores provide additional avenues for further progress in vivo bioimaging. Based on the development of chemical materials and physical optoelectronics, new NIR-II microscopy techniques are emerging, such as confocal and multiphoton microscopy, light-sheet fluorescence microscopy (LSFM), and wide-field microscopy. In this review, we introduce the characteristics of in vivo imaging using NIR-II fluorescence microscopy. We also cover the recent advances in NIR-II fluorescence microscopy techniques in bioimaging and the potential for overcoming current challenges.
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Affiliation(s)
- Tian Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingying Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mingfu Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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16
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Cao R, Zhao J, Li L, Du L, Zhang Y, Luo Y, Jiang L, Davis S, Zhou Q, de la Zerda A, Wang LV. Optical-resolution photoacoustic microscopy with a needle-shaped beam. NATURE PHOTONICS 2023; 17:89-95. [PMID: 38149029 PMCID: PMC10751030 DOI: 10.1038/s41566-022-01112-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/19/2022] [Indexed: 12/28/2023]
Abstract
Optical-resolution photoacoustic microscopy (OR-PAM) can visualize wavelength-dependent optical absorption at the cellular level. However, OR-PAM suffers from a limited depth of field (DOF) due to the tight focus of the optical excitation beam, making it challenging to acquire high-resolution images of samples with uneven surfaces or high-quality volumetric images without z-scanning. To overcome this limitation, we propose needle-shaped beam photoacoustic microscopy (NB-PAM), which can extend the DOF to up to ~28-fold Rayleigh lengths via customized diffractive optical elements (DOEs). The DOE generate a needle beam with a well-maintained beam diameter, a uniform axial intensity distribution, and negligible sidelobes. The advantage of using NB-PAM is demonstrated by both histology-like imaging of fresh slide-free organs using a 266 nm laser and in vivo mouse brain vasculature imaging using a 532 nm laser. The approach provides new perspectives for slide-free intraoperative pathological imaging and in-vivo organ-level imaging.
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Affiliation(s)
- Rui Cao
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Jingjing Zhao
- Department of Structural Biology, Stanford University School of Medicine, Stanford University, Stanford, California, USA
| | - Lei Li
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Lin Du
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yide Zhang
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Yilin Luo
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Laiming Jiang
- Department of Biomedical Engineering and Ophthalmology, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
| | - Samuel Davis
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Qifa Zhou
- Department of Biomedical Engineering and Ophthalmology, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
| | - Adam de la Zerda
- Department of Structural Biology, Stanford University School of Medicine, Stanford University, Stanford, California, USA
- Biophysics Program, Molecular Imaging Program, and Bio-X Program at Stanford University, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Lihong V Wang
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, Pasadena, California, USA
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17
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Liu Z, Zhu Y, Zhang L, Jiang W, Liu Y, Tang Q, Cai X, Li J, Wang L, Tao C, Yin X, Li X, Hou S, Jiang D, Liu K, Zhou X, Zhang H, Liu M, Fan C, Tian Y. Structural and functional imaging of brains. Sci China Chem 2022; 66:324-366. [PMID: 36536633 PMCID: PMC9753096 DOI: 10.1007/s11426-022-1408-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/28/2022] [Indexed: 12/23/2022]
Abstract
Analyzing the complex structures and functions of brain is the key issue to understanding the physiological and pathological processes. Although neuronal morphology and local distribution of neurons/blood vessels in the brain have been known, the subcellular structures of cells remain challenging, especially in the live brain. In addition, the complicated brain functions involve numerous functional molecules, but the concentrations, distributions and interactions of these molecules in the brain are still poorly understood. In this review, frontier techniques available for multiscale structure imaging from organelles to the whole brain are first overviewed, including magnetic resonance imaging (MRI), computed tomography (CT), positron emission tomography (PET), serial-section electron microscopy (ssEM), light microscopy (LM) and synchrotron-based X-ray microscopy (XRM). Specially, XRM for three-dimensional (3D) imaging of large-scale brain tissue with high resolution and fast imaging speed is highlighted. Additionally, the development of elegant methods for acquisition of brain functions from electrical/chemical signals in the brain is outlined. In particular, the new electrophysiology technologies for neural recordings at the single-neuron level and in the brain are also summarized. We also focus on the construction of electrochemical probes based on dual-recognition strategy and surface/interface chemistry for determination of chemical species in the brain with high selectivity and long-term stability, as well as electrochemophysiological microarray for simultaneously recording of electrochemical and electrophysiological signals in the brain. Moreover, the recent development of brain MRI probes with high contrast-to-noise ratio (CNR) and sensitivity based on hyperpolarized techniques and multi-nuclear chemistry is introduced. Furthermore, multiple optical probes and instruments, especially the optophysiological Raman probes and fiber Raman photometry, for imaging and biosensing in live brain are emphasized. Finally, a brief perspective on existing challenges and further research development is provided.
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Affiliation(s)
- Zhichao Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241 China
| | - Ying Zhu
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Liming Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241 China
| | - Weiping Jiang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071 China
| | - Yawei Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 China
| | - Qiaowei Tang
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Xiaoqing Cai
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Jiang Li
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Lihua Wang
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Changlu Tao
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | | | - Xiaowei Li
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Shangguo Hou
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055 China
| | - Dawei Jiang
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Kai Liu
- Department of Chemistry, Tsinghua University, Beijing, 100084 China
| | - Xin Zhou
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071 China
| | - Hongjie Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 China
- Department of Chemistry, Tsinghua University, Beijing, 100084 China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241 China
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18
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Niazi A, Parvin P, Jafargholi A, Basam MA, Khodabakhshi Z, Bavali A, Kamyab Hesari K, Sohrabizadeh Z, Hassanzadeh T, Shirafkan Dizaj L, Amiri R, Heidari O, Aghaei M, Atyabi F, Ehtesham A, Moafi A. Discrimination of normal and cancerous human skin tissues based on laser-induced spectral shift fluorescence microscopy. Sci Rep 2022; 12:20927. [PMID: 36463297 PMCID: PMC9719548 DOI: 10.1038/s41598-022-25055-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/23/2022] [Indexed: 12/07/2022] Open
Abstract
A homemade spectral shift fluorescence microscope (SSFM) is coupled with a spectrometer to record the spectral images of specimens based on the emission wavelength. Here a reliable diagnosis of neoplasia is achieved according to the spectral fluorescence properties of ex-vivo skin tissues after rhodamine6G (Rd6G) staining. It is shown that certain spectral shifts occur for nonmelanoma/melanoma lesions against normal/benign nevus, leading to spectral micrographs. In fact, there is a strong correlation between the emission wavelength and the sort of skin lesions, mainly due to the Rd6G interaction with the mitochondria of cancerous cells. The normal tissues generally enjoy a significant red shift regarding the laser line (37 nm). Conversely, plenty of fluorophores are conjugated to unhealthy cells giving rise to a relative blue shift i.e., typically SCC (6 nm), BCC (14 nm), and melanoma (19 nm) against healthy tissues. In other words, the redshift takes place with respect to the excitation wavelength i.e., melanoma (18 nm), BCC (23 nm), and SCC (31 nm) with respect to the laser line. Consequently, three data sets are available in the form of micrographs, addressing pixel-by-pixel signal intensity, emission wavelength, and fluorophore concentration of specimens for prompt diagnosis.
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Affiliation(s)
- A. Niazi
- grid.411368.90000 0004 0611 6995Department of Physics and Energy Engineering, Amirkabir University of Technology, P.O. Box 15875-4413, Tehran, Iran
| | - P. Parvin
- grid.411368.90000 0004 0611 6995Department of Physics and Energy Engineering, Amirkabir University of Technology, P.O. Box 15875-4413, Tehran, Iran
| | - A. Jafargholi
- grid.411368.90000 0004 0611 6995Department of Physics and Energy Engineering, Amirkabir University of Technology, P.O. Box 15875-4413, Tehran, Iran ,grid.83440.3b0000000121901201Department of Electronic and Electrical Engineering, University College London (UCL), London, England, UK
| | - M. A. Basam
- grid.411368.90000 0004 0611 6995Department of Physics and Energy Engineering, Amirkabir University of Technology, P.O. Box 15875-4413, Tehran, Iran
| | - Z. Khodabakhshi
- grid.440804.c0000 0004 0618 762XFaculty of Physics, Shahrood University of Technology, Shahrood, Iran
| | - A. Bavali
- grid.411368.90000 0004 0611 6995Department of Physics and Energy Engineering, Amirkabir University of Technology, P.O. Box 15875-4413, Tehran, Iran
| | - K. Kamyab Hesari
- grid.411705.60000 0001 0166 0922Department of Dermatopathology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Z. Sohrabizadeh
- grid.411368.90000 0004 0611 6995Department of Physics and Energy Engineering, Amirkabir University of Technology, P.O. Box 15875-4413, Tehran, Iran
| | - T. Hassanzadeh
- grid.411368.90000 0004 0611 6995Department of Physics and Energy Engineering, Amirkabir University of Technology, P.O. Box 15875-4413, Tehran, Iran
| | - L. Shirafkan Dizaj
- grid.411368.90000 0004 0611 6995Department of Physics and Energy Engineering, Amirkabir University of Technology, P.O. Box 15875-4413, Tehran, Iran
| | - R. Amiri
- grid.415733.7Department of Pathology, Razi Hospital, POX:1199663911, Tehran, Iran
| | - O. Heidari
- grid.411368.90000 0004 0611 6995Department of Physics and Energy Engineering, Amirkabir University of Technology, P.O. Box 15875-4413, Tehran, Iran
| | - M. Aghaei
- grid.411368.90000 0004 0611 6995Department of Physics and Energy Engineering, Amirkabir University of Technology, P.O. Box 15875-4413, Tehran, Iran ,grid.5947.f0000 0001 1516 2393Department of Ocean Operations and Civil Engineering, Norwegian University of Science and Technology (NTNU), 6009 Ålesund, Norway
| | - F. Atyabi
- grid.411705.60000 0001 0166 0922Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - A. Ehtesham
- grid.4367.60000 0001 2355 7002Radiation Oncology Department, School of Medicine Washington University, St. Louis, USA
| | - A. Moafi
- grid.411368.90000 0004 0611 6995Department of Physics and Energy Engineering, Amirkabir University of Technology, P.O. Box 15875-4413, Tehran, Iran
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Affiliation(s)
- Douglas J Taatjes
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA.
| | - Jürgen Roth
- University of Zurich, 8091, Zurich, Switzerland
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20
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Gunzer M. Fast volumetric scanning of living tissue. Nat Biomed Eng 2022; 6:497-498. [PMID: 35578007 DOI: 10.1038/s41551-022-00894-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Matthias Gunzer
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, Germany. .,Leibniz Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany.
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21
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McKenzie AT, Woodoff-Leith E, Dangoor D, Cervera A, Ressler HW, Whitney K, Dams-O'Connor K, Wu Z, Hillman EMC, Seifert AC, Crary JF. Ex situ perfusion fixation for brain banking: a technical report. FREE NEUROPATHOLOGY 2022; 3:3-22. [PMID: 37284166 PMCID: PMC10209847 DOI: 10.17879/freeneuropathology-2022-4368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/20/2022] [Indexed: 06/08/2023]
Abstract
Perfusion fixation is a well-established technique in animal research to improve preservation quality in the study of many tissues, including the brain. There is a growing interest in using perfusion to fix postmortem human brain tissue to achieve the highest fidelity preservation for downstream high-resolution morphomolecular brain mapping studies. Numerous practical barriers arise when applying perfusion fixation in brain banking settings, including the large mass of the organ, degradation of vascular integrity and patency prior to the start of the procedure, and differing investigator goals sometimes necessitating part of the brain to be frozen. As a result, there is a critical need to establish a perfusion fixation procedure in brain banking that is flexible and scalable. This technical report describes our approach to developing an ex situ perfusion fixation protocol. We discuss the challenges encountered and lessons learned while implementing this procedure. Routine morphological staining and RNA in situ hybridization data show that the perfused brains have well-preserved tissue cytoarchitecture and intact biomolecular signal. However, it remains uncertain whether this procedure leads to improved histology quality compared to immersion fixation. Additionally, ex vivo magnetic resonance imaging (MRI) data suggest that the perfusion fixation protocol may introduce imaging artifacts in the form of air bubbles in the vasculature. We conclude with further research directions to investigate the use of perfusion fixation as a rigorous and reproducible alternative to immersion fixation for the preparation of postmortem human brains.
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Affiliation(s)
- Andrew T. McKenzie
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emma Woodoff-Leith
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Diana Dangoor
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alessandra Cervera
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hadley Walsh Ressler
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kristen Whitney
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kristen Dams-O'Connor
- Department of Rehabilitation and Human Performance, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zhuhao Wu
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Elizabeth M. C. Hillman
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology and the Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, New York, USA
| | - Alan C. Seifert
- Biomedical Engineering and Imaging Institute, Department of Diagnostic, Molecular and Interventional Radiology, and Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John F. Crary
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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