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Xu X, Su J, Zhu R, Li K, Zhao X, Fan J, Mao F. From morphology to single-cell molecules: high-resolution 3D histology in biomedicine. Mol Cancer 2025; 24:63. [PMID: 40033282 PMCID: PMC11874780 DOI: 10.1186/s12943-025-02240-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2024] [Accepted: 01/18/2025] [Indexed: 03/05/2025] Open
Abstract
High-resolution three-dimensional (3D) tissue analysis has emerged as a transformative innovation in the life sciences, providing detailed insights into the spatial organization and molecular composition of biological tissues. This review begins by tracing the historical milestones that have shaped the development of high-resolution 3D histology, highlighting key breakthroughs that have facilitated the advancement of current technologies. We then systematically categorize the various families of high-resolution 3D histology techniques, discussing their core principles, capabilities, and inherent limitations. These 3D histology techniques include microscopy imaging, tomographic approaches, single-cell and spatial omics, computational methods and 3D tissue reconstruction (e.g. 3D cultures and spheroids). Additionally, we explore a wide range of applications for single-cell 3D histology, demonstrating how single-cell and spatial technologies are being utilized in the fields such as oncology, cardiology, neuroscience, immunology, developmental biology and regenerative medicine. Despite the remarkable progress made in recent years, the field still faces significant challenges, including high barriers to entry, issues with data robustness, ambiguous best practices for experimental design, and a lack of standardization across methodologies. This review offers a thorough analysis of these challenges and presents recommendations to surmount them, with the overarching goal of nurturing ongoing innovation and broader integration of cellular 3D tissue analysis in both biology research and clinical practice.
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Affiliation(s)
- Xintian Xu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center, Peking University Third Hospital, Beijing, China
- Department of Biochemistry and Molecular Biology, Beijing, Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jimeng Su
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center, Peking University Third Hospital, Beijing, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Rongyi Zhu
- Department of Biochemistry and Molecular Biology, Beijing, Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Kailong Li
- Department of Biochemistry and Molecular Biology, Beijing, Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xiaolu Zhao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and GynecologyNational Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital)Key Laboratory of Assisted Reproduction (Peking University), Ministry of EducationBeijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Peking University Third Hospital, Beijing, China.
| | - Jibiao Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China.
- Cancer Center, Peking University Third Hospital, Beijing, China.
- Beijing Key Laboratory for Interdisciplinary Research in Gastrointestinal Oncology (BLGO), Beijing, China.
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Su S, Liu YM, Zhan LP, Gao SY, He C, Zhang Q, Huang XF. Evaluation of the accuracy of cone-beam computed tomography image segmentation of isolated tooth roots based on the dynamic threshold method. BMC Oral Health 2023; 23:752. [PMID: 37833773 PMCID: PMC10571368 DOI: 10.1186/s12903-023-03423-y] [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: 07/12/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023] Open
Abstract
OBJECTIVE Accurate quantification of the root surface area (RSA) plays a decisive role in the advancement of periodontal, orthodontic, and restorative treatment modalities. In this study, we aimed to develop a dynamic threshold-based computer-aided system for segmentation and calculation of the RSA of isolated teeth on cone-beam computed tomography (CBCT) and to assess the accuracy of the measured data. METHOD We selected 24 teeth to be extracted, including single-rooted and multi-rooted teeth, from 22 patients who required tooth extraction. In the experimental group, we scanned 24 isolated teeth using CBCT with a voxel size of 0.3 mm. We designed a computer-aided system based on a personalized dynamic threshold algorithm to automatically segment the roots of 24 isolated teeth in CBCT images and calculate the RSA. In the control group, we employed digital intraoral scanner devices to perform optical scanning on 24 isolated teeth and subsequently manually segmented the roots using 3-matic software to calculate the RSA. We used the paired t-test (P < 0.05) and Bland-Altman plots to analyze the consistency of the two measurement methods. RESULTS The results of the paired t-test showed that there was no significant difference in the RSAs obtained using the dynamic threshold method and the optical scanning image reconstruction (t = 1.005, P = 0.325 > 0.05). As per the Bland-Altman plot, the results were evenly distributed within the region of ± 1.96 standard deviations of the mean, with no increasing or decreasing trends and good consistency. CONCLUSION In this study, we designed a computer-aided root segmentation system based on a personalized dynamic threshold algorithm to automatically segment the roots of isolated teeth in CBCT images with a voxel size of 0.3 mm. We found that the RSA calculated using this approach was highly accurate, and a voxel of 0.3 mm in size could accurately display the surface area data in CBCT images. Overall, our findings in this study provide a foundation for future work on accurate automatic segmentation of tooth roots in full-mouth CBCT images and the computation of RSA.
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Affiliation(s)
- Sha Su
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, 95 Yong 'an Road, Xicheng District, Beijing, 100050, China
| | - Yu-Meng Liu
- Department of General surgery, Beijing Huaxin Hospital, the First Affiliated Hospital of Tsinghua University, Beijing, 100016, China
| | - Li-Ping Zhan
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, 95 Yong 'an Road, Xicheng District, Beijing, 100050, China
| | - Si-Yuan Gao
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, 95 Yong 'an Road, Xicheng District, Beijing, 100050, China
| | - Cai He
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, 95 Yong 'an Road, Xicheng District, Beijing, 100050, China
| | - Qing Zhang
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, 95 Yong 'an Road, Xicheng District, Beijing, 100050, China
| | - Xiao-Feng Huang
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, 95 Yong 'an Road, Xicheng District, Beijing, 100050, China.
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Kurz B, Schreiver I, Siewert K, Haslböck B, Weiß KT, Hannemann J, Berner B, von Eichborn MI, Berneburg M, Bäumler W. Investigation of Adverse Reactions in Tattooed Skin through Histological and Chemical Analysis. Dermatology 2023; 239:782-793. [PMID: 37231944 PMCID: PMC10614264 DOI: 10.1159/000530949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 05/02/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Just as the number of tattooed people has increased in recent years, so has the number of adverse reactions in tattooed skin. Tattoo colourants contain numerous, partly unidentified substances, which have the potential to provoke adverse skin reactions like allergies or granulomatous reactions. Identification of the triggering substances is often difficult or even impossible. METHODS Ten patients with typical adverse reactions in tattooed skin were enrolled in the study. Skin punch biopsies were taken and the paraffin-embedded specimens were analysed by standard haematoxylin and eosin and anti-CD3 stainings. Tattoo colourants provided by patients and punch biopsies of patients were analysed with different chromatography and mass spectrometry methods and X-ray fluorescence. Blood samples of 2 patients were screened for angiotensin-converting enzyme (ACE) and soluble interleukin-2 receptor (sIL-2R). RESULTS Histology showed variable skin reactions such as eosinophilic infiltrate, granulomatous reactions, or pseudolymphoma. CD3+ T lymphocytes dominated the dermal cellular infiltrate. Most patients had adverse skin reactions in red tattoos (n = 7), followed by white tattoos (n = 2). The red tattooed skin areas predominantly contained Pigment Red (P.R.) 170, but also P.R. 266, Pigment Orange (P.O.) 13, P.O. 16, and Pigment Blue (P.B.) 15. The white colourant of 1 patient contained rutile titanium dioxide but also other metals like nickel and chromium and methyl dehydroabietate - known as the main ingredient of colophonium. None of the 2 patients showed increased levels of ACE and sIL-2R related to sarcoidosis. Seven of the study participants showed partial or complete remission after treatment with topical steroids, intralesional steroids, or topical tacrolimus. CONCLUSIONS The combination of the methods presented might be a rational approach to identify the substances that trigger adverse reactions in tattoos. Such an approach might help make tattoo colourants safer in the future if such trigger substances could be omitted.
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Affiliation(s)
- Bernadett Kurz
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
| | - Ines Schreiver
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Katherina Siewert
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Birgit Haslböck
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
| | - Katharina T. Weiß
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
| | - Julia Hannemann
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
| | - Bianca Berner
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
| | | | - Mark Berneburg
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
| | - Wolfgang Bäumler
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
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Schubert S, Kluger N, Schreiver I. Hypersensitivity to permanent tattoos: Literature summary and comprehensive review of patch tested tattoo patients 1997-2022. Contact Dermatitis 2023; 88:331-350. [PMID: 36772861 DOI: 10.1111/cod.14291] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 02/01/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
We outline constituents of tattoo and permanent make-up ink with regard to inflammatory tattoo reactions and population-based confounders. The comprehensive review of patch-tested tattoo patients between 1997 and 2022 shows that tattoo allergy cannot be reliably diagnosed via patch testing with today's knowledge. Weak penetration and slow haptenization of pigments, unavailability of pigments as test allergens and a lack of knowledge concerning relevant epitopes hamper the diagnosis of tattoo allergy. Patch testing p-phenylenediamine and disperse (textile) dyes is not able to close this gap. Sensitization to metals was associated with all types of tattoo complications, although often not clinically relevant for the tattoo reaction. Binders and industrial biocides are frequently missing on ink declarations and should be patch tested. The pigment carbon black (C.I. 77266) is no skin sensitizer. Patch tests with culprit inks were usually positive with cheap ink products for non-professional use or with professionally used inks in patients with eczematous reactions characterized by papules and infiltration. Tape stripping before patch testing and patch test readings on Day 8 or 10 may improve the diagnostic quality. The meaningfulness of the categorical EU-wide ban of Pigment Green 7 and Pigment Blue 15:3 is not substantiated by the presented data.
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Affiliation(s)
- Steffen Schubert
- Information Network of Departments of Dermatology (IVDK), Institute at the University Medical Center Göttingen, Göttingen, Germany
| | - Nicolas Kluger
- Department of Dermatology, 'Tattoo' Consultation, Bichat-Claude Bernard Hospital, Assistance Publique - Hôpitaux de Paris, Paris, France.,Department of Dermatology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Ines Schreiver
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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den Blanken MD, van der Bent S, Liberton N, Grimbergen M, Hofman MBM, Verdaasdonk R, Rustemeyer T. Quantification of cutaneous allergic reactions using 3D optical imaging: A feasibility study. Skin Res Technol 2019; 26:67-75. [PMID: 31423660 PMCID: PMC7003777 DOI: 10.1111/srt.12765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 06/28/2019] [Indexed: 11/29/2022]
Abstract
Background User‐independent quantitative measures of cutaneous allergic reactions can help the physicians manage and evaluate the treatment of cutaneous allergic reactions. In this paper, we present and validate a method to quantify the elevation, volume and area of cutaneous allergic reactions to red tattoos. Methods The skin surface of allergic tattoo reactions was imaged using an optical 3D scanner. The in‐house developed analysis tool measured the elevation, volume and area of the lesions, compared to a reference surface. This reference surface was created by 3D interpolation of the skin after manual removal of the lesions. The error of the interpolation tool was validated using a digital arm model. The error of our optical scanner was determined using a 3D printed lesion phantom. The clinical feasibility of the method was tested in 83 lesions in 17 patients. Results The method showed clear potential to assess skin elevation, volume change and area of an allergic reaction. The validation measurements revealed that the error due to interpolation increases for larger interpolation areas and largely determined the error in the clinical measurements. Lesions with a width ≥4 mm and an elevation ≥0.4 mm could be measured with an error below 26%. Patient measurements showed that lesions up to 600 mm2 could be measured accurately, and elevation and volume changes could be assessed at follow‐up. Conclusion Quantification of cutaneous allergic reactions to red tattoos using 3D optical scanning is feasible and may objectify skin elevation and improve management of the allergic reaction.
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Affiliation(s)
- Mark D den Blanken
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, location VUmc, Amsterdam, The Netherlands
| | - Sebastiaan van der Bent
- Department of Dermatology, Academic Tattoo Clinic Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Niels Liberton
- Medical Technology, 3D innovationlab, Amsterdam UMC, location VUmc, Amsterdam, The Netherlands
| | - Matthijs Grimbergen
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, location VUmc, Amsterdam, The Netherlands
| | - Mark B M Hofman
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, location VUmc, Amsterdam, The Netherlands
| | - Ruud Verdaasdonk
- Biomedical Photonics and Imaging group, TechMed Center, University of Twente, Amsterdam, The Netherlands
| | - Thomas Rustemeyer
- Department of Dermatology, Academic Tattoo Clinic Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
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