Routine Optical Clearing of 3D-Cell Cultures: Simplicity Forward
Open accessAbstract
Three-dimensional cell cultures, such as spheroids and organoids, serve as increasingly important models in fundamental and applied research and start to be used for drug screening purposes. Optical tissue clearing procedures are employed to enhance visualization of fluorescence-stained organs, tissues, and three-dimensional cell cultures. To get a more systematic overview about the effects and applicability of optical tissue clearing on three-dimensional cell cultures, we compared six different clearing/embedding protocols on seven types of spheroid- and chip-based three-dimensional cell cultures of approximately 300 μm in size that were stained with nuclear dyes, immunofluorescence, cell trackers, and cyan fluorescent protein. Subsequent whole mount confocal microscopy and semi-automated image analysis were performed to quantify the effects. Quantitative analysis included fluorescence signal intensity and signal-to-noise ratio as a function of z-depth as well as segmentation and counting of nuclei and immunopositive cells. In general, these analyses revealed five key points, which largely confirmed current knowledge and were quantified in this study. First, there was a massive variability of effects of different clearing protocols on sample transparency and shrinkage as well as on dye quenching. Second, all tested clearing protocols worked more efficiently on samples prepared with one cell type than on co-cultures. Third, z-compensation was imperative to minimize variations in signal-to-noise ratio. Fourth, a combination of sample-inherent cell density, sample shrinkage, uniformity of signal-to-noise ratio, and image resolution had a strong impact on data segmentation, cell counts, and relative numbers of immunofluorescence-positive cells. Finally, considering all mentioned aspects and including a wish for simplicity and speed of protocols - in particular, for screening purposes - clearing with 88% Glycerol appeared to be the most promising option amongst the ones tested.
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Specialized microscopy techniques and tissue processing (e.g., clearing) can overcome challenges in imaging 3D cultures, but they require additional specifications and QC.
“Specialized microscopy techniques and tissue processing (e.g., clearing) can overcome these challenges, but they require additional specifications and QC (Nurnberg et al., 2020; Renner et al., 2021; Cheng et al., 2023; Yoshida et al., 2020; Kahn-Krell et al., 2022).”
From Recommendations on fit-for-purpose criteria to establish quality management for microphysiological systems and for monitoring their reproducibility (2024) · cites this paper as Nurnberg et al., 2020
The Introduction (page unavailable) says whole-mount confocal or light-sheet imaging can circumvent limitations of sectioning, and that clearing improves imaging depth. The Conclusion (page unavailable) says clearing protocols must be chosen according to sample characteristics and that imaging settings affect quantitative analysis. The paper supports the need for method-specific planning, but does not explicitly say these techniques require additional specifications and quality control. (LLM, conf=0.82)
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Fiji: an open-source platform for biological-image analysis
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2019 · Cited by 66,890 · see citing works
Cerebral organoids model human brain development and microcephaly
Lancaster, M. A., Renner, M., Martin, C.-A., Wenzel, D., Bicknell, L. S., Hurles, M. E., Homfray, T., Penninger, J. M., Jackson, A. P., & Knoblich, J. A. (2013) · Nature · doi:10.1038/nature12517 · Cited by 5,372 · see citing works
Structural and molecular interrogation of intact biological systems
Chung, K., Wallace, J., Kim, S.-Y., Kalyanasundaram, S., Andalman, A. S., Davidson, T. J., Mirzabekov, J. J., Zalocusky, K. A., Mattis, J., Denisin, A. K., et al. (2013) · Nature · doi:10.1038/nature12107 · Cited by 2,008 · see citing works
Modeling physiological events in 2D vs. 3D cell culture
Duval, K., Grover, H., Han, L.-H., Mou, Y., Pegoraro, A. F., Fredberg, J., & Chen, Z. (2017) · Physiology · doi:10.1152/physiol.00036.2016 · Cited by 1,849 · cited 1× · see citing works
“The absence of nutrient and oxygen gradients, as well as restricted migration potential grown on a plastic surface, further contribute to a limited representation of physiology in 2D in vitro systems (Duval et al., 2017).”
BackgroundiDISCO: A Simple, Rapid Method to Immunolabel Large Tissue Samples for Volume Imaging
Renier, N., Wu, Z., Simon, D. J., Yang, J. H., Ariel, P., & Tessier‐Lavigne, M. (2014) · Cell · doi:10.1016/j.cell.2014.10.010 · Cited by 1,838 · see citing works
Drost, J., & Clevers, H. (2018) · Nature Reviews Cancer · doi:10.1038/s41568-018-0007-6 · Cited by 1,790 · see citing works
Chen, F., Tillberg, P. W., & Boyden, E. S. (2015) · Science · doi:10.1126/science.1260088 · Cited by 1,531 · see citing works
Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis
Susaki, E. A., Tainaka, K., Perrin, D., Kishino, F., Tawara, T., Watanabe, T. M., Yokoyama, C., Onoe, H., Eguchi, M., Yamaguchi, S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.03.042 · Cited by 1,300 · see citing works
Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain
Dodt, H., Leischner, U., Schierloh, A., Jährling, N., Mauch, C. P., Deininger, K., Deussing, J. M., Eder, M., Zieglgänsberger, W., & Becker, K. (2007) · Nature Methods · doi:10.1038/nmeth1036 · Cited by 1,240 · see citing works
Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain
Hama, H., Kurokawa, H., Kawano, H., Ando, R., Shimogori, T., Noda, H., Fukami, K., Sakaue-Sawano, A., & Miyawaki, A. (2011) · Nature Neuroscience · doi:10.1038/nn.2928 · Cited by 1,147 · see citing works
Richardson, D. S., & Lichtman, J. W. (2015) · Cell · doi:10.1016/j.cell.2015.06.067 · Cited by 1,095 · see citing works
Three-dimensional imaging of solvent-cleared organs using 3DISCO
Ertürk, A., Becker, K., Jährling, N., Mauch, C. P., Hojer, C. D., Egen, J. G., Hellal, F., Bradke, F., Sheng, M., & Dodt, H. (2012) · Nature Protocols · doi:10.1038/nprot.2012.119 · Cited by 997 · see citing works
Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing
Yang, B., Treweek, J. B., Kulkarni, R. P., Deverman, B. E., Chen, C., Lubeck, E., Shah, S., Cai, L., & Gradinaru, V. (2014) · Cell · doi:10.1016/j.cell.2014.07.017 · Cited by 933 · see citing works
SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction
Ke, M., Fujimoto, S., & Imai, T. (2013) · Nature Neuroscience · doi:10.1038/nn.3447 · Cited by 895 · see citing works
Comparison of 2D- and 3D-culture models as drug-testing platforms in breast cancer
IMAMURA, Y., MUKOHARA, T., SHIMONO, Y., FUNAKOSHI, Y., CHAYAHARA, N., TOYODA, M., KIYOTA, N., TAKAO, S., KONO, S., NAKATSURA, T., et al. (2015) · Oncology Reports · doi:10.3892/or.2015.3767 · Cited by 845 · see citing works
Shrinkage-mediated imaging of entire organs and organisms using uDISCO
Pan, C., Cai, R., Quacquarelli, F. P., Ghasemigharagoz, A., Lourbopoulos, A. I., Matryba, P., Plesnila, N., Dichgans, M., Hellal, F., & Ertürk, A. (2016) · Nature Methods · doi:10.1038/nmeth.3964 · Cited by 609 · see citing works
ScaleS: an optical clearing palette for biological imaging
Hama, H., Hioki, H., Namiki, K., Hoshida, T., Kurokawa, H., Ishidate, F., Kaneko, T., Akagi, T., Saito, T., Saido, T. C., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.4107 · Cited by 584 · see citing works
Tsai, P. S., Kaufhold, J. P., Blinder, P., Friedman, B., Drew, P. J., Karten, H. J., Lyden, P. D., & Kleinfeld, D. (2009) · Journal of Neuroscience · doi:10.1523/jneurosci.3287-09.2009 · Cited by 575 · see citing works
Simple, Scalable Proteomic Imaging for High-Dimensional Profiling of Intact Systems
Murray, E. M., Cho, J., Goodwin, D., Ku, T., Swaney, J., Kim, S., Choi, H., Park, Y.-G., Park, J. Y., Hubbert, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.025 · Cited by 470 · see citing works
Optical scattering properties of soft tissue: a discrete particle model
Schmitt, J. M., & Kumar, G. (1998) · Applied Optics · doi:10.1364/ao.37.002788 · Cited by 411 · see citing works
ClearT: a detergent- and solvent-free clearing method for neuronal and non-neuronal tissue
Kuwajima, T., Sitko, A. A., Bhansali, P., Jurgens, C., Guido, W., & Mason, C. A. (2013) · Development · doi:10.1242/dev.091844 · Cited by 400 · see citing works
Self‐organized developmental patterning and differentiation in cerebral organoids
Renner, M., Lancaster, M. A., Bian, S., Choi, H., Ku, T., Peer, A., Chung, K., & Knoblich, J. A. (2017) · The EMBO Journal · doi:10.15252/embj.201694700 · Cited by 389 · see citing works
Optical sectioning microscopy with planar or structured illumination
Mertz, J. C. (2011) · Nature Methods · doi:10.1038/nmeth.1709 · Cited by 350 · see citing works
Luca, A. C., Mersch, S., Deenen, R., Schmidt, S., Messner, I., Schäfer, K.-L., Baldus, S. E., Huckenbeck, W., Piekorz, R. P., Knoefel, W. T., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0059689 · Cited by 341 · see citing works
Chemical Principles in Tissue Clearing and Staining Protocols for Whole-Body Cell Profiling
Tainaka, K., Kuno, A., Kubota, S. I., Murakami, T. C., & Ueda, H. R. (2016) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-111315-125001 · Cited by 280 · see citing works
Bauer, S., Wennberg Huldt, C., Kanebratt, K. P., Durieux, I., Gunne, D., Andersson, S., Ewart, L., Haynes, W. G., Maschmeyer, I., Winter, A., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-14815-w · Cited by 272 · see citing works
Super-Resolution Mapping of Neuronal Circuitry With an Index-Optimized Clearing Agent
Ke, M., Nakai, Y., Fujimoto, S., Takayama, R., Yoshida, S. M., Kitajima, T. S., Sato, M., & Imai, T. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.02.057 · Cited by 266 · see citing works
Wenzel, C., Riefke, B., Gründemann, S., Krebs, A., Christian, S., Prinz, F., Osterland, M., Golfier, S., Raese, S., Ansari, N., et al. (2014) · Experimental Cell Research · doi:10.1016/j.yexcr.2014.01.017 · Cited by 257 · see citing works
Li, W., Germain, R. N., & Gerner, M. Y. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1708981114 · Cited by 251 · see citing works
State-of-the-art of 3D cultures (organs-on-a-chip) in safety testing and pathophysiology
Alépée, N. (2014) · ALTEX · doi:10.14573/altex1406111 · Cited by 221 · see citing works
Lee, C., Bendriem, R. M., Wu, W. W., & Shen, R. (2017) · Journal of Biomedical Science · doi:10.1186/s12929-017-0362-8 · Cited by 198 · see citing works
Three-dimensional in vitro cancer models: a short review
Wang, C., Tang, Z., Zhao, Y., Yao, R., Li, L., & Sun, W. (2014) · Biofabrication · doi:10.1088/1758-5082/6/2/022001 · Cited by 173 · see citing works
Scalable and DiI-compatible optical clearance of the mammalian brain
Hou, B., Zhang, D., Zhao, S., Wei, M., Yang, Z., Wang, S., Wang, J., Zhang, X., Liu, B., Fan, L., et al. (2015) · Frontiers in Neuroanatomy · doi:10.3389/fnana.2015.00019 · Cited by 171 · see citing works
Clearing of fixed tissue: a review from a microscopist’s perspective
Silvestri, L., Costantini, I., Sacconi, L., & Pavone, F. S. (2016) · Journal of Biomedical Optics · doi:10.1117/1.jbo.21.8.081205 · Cited by 148 · see citing works
The Role of Tumor Microenvironment in Chemoresistance: 3D Extracellular Matrices as Accomplices
Senthebane, D. A., Jonker, T., Rowe, A., Thomford, N. E., Munro, D., Dandara, C., Wonkam, A., Govender, D., Calder, B., Soares, N. C., et al. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19102861 · Cited by 133 · see citing works
Three-Dimensional Neural Spheroid Culture: An In Vitro Model for Cortical Studies
Dingle, Y. L., Boutin, M. E., Chirila, A. M., Livi, L. L., Labriola, N. R., Jakubek, L. M., Morgan, J. R., Darling, E. M., Kauer, J. A., & Hoffman–Kim, D. (2015) · Tissue Engineering Part C Methods · doi:10.1089/ten.tec.2015.0135 · Cited by 132 · see citing works
Zschenker, O., Streichert, T., Hehlgans, S., & Cordes, N. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034279 · Cited by 129 · see citing works
A beginner’s guide to tissue clearing
Ariel, P. (2017) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2016.12.009 · Cited by 129 · see citing works
In Vitro Tissue‐Engineered Skeletal Muscle Models for Studying Muscle Physiology and Disease
Khodabukus, A., Prabhu, N. K., Wang, J., & Bursac, N. (2018) · Advanced Healthcare Materials · doi:10.1002/adhm.201701498 · Cited by 128 · see citing works
Fong, E. L. S., Wan, X., Yang, J., Morgado, M., Mikos, A. G., Harrington, D. A., Navone, N. M., & Farach‐Carson, M. C. (2015) · Biomaterials · doi:10.1016/j.biomaterials.2015.10.059 · Cited by 111 · see citing works
Grootjans, J., Hundscheid, I. H. R., Lenaerts, K., Boonen, B., Renes, I. B., Verheyen, F., Dejong, C. H. C., MEYENFELDT, M. F. V., Beets, G. L., & Buurman, W. A. (2012) · Gut · doi:10.1136/gutjnl-2011-301956 · Cited by 109 · see citing works
Insect NMDA receptors mediate juvenile hormone biosynthesis
Chiang, A., Lin, W., Liu, H.-P., Pszczółkowski, M. A., Fu, T., Chiu, S., & Holbrook, G. L. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.012318899 · Cited by 103 · see citing works
A high-throughput imaging and nuclear segmentation analysis protocol for cleared 3D culture models
Boutin, M. E., Voss, T. C., Titus, S. A., Cruz-Gutierrez, K., Michael, S., & Ferrer, M. (2018) · Scientific Reports · doi:10.1038/s41598-018-29169-0 · Cited by 100 · see citing works
Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space
Toyoshima, Y., Tokunaga, T., Hirose, O., Kanamori, M., Teramoto, T., Jang, M., Kuge, S., Ishihara, T., Yoshida, R., & Iino, Y. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004970 · Cited by 79 · see citing works
Hübner, J., Raschke, M., Rütschle, I., Gräßle, S., Hasenberg, T., Schirrmann, K., Lorenz, A., Schnurre, S., Lauster, R., Maschmeyer, I., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-33462-3 · Cited by 76 · see citing works
Pitfalls in Diagnostic Immunohistology
Leong, A. S. ‐. (2004) · Advances in Anatomic Pathology · doi:10.1097/00125480-200403000-00002 · Cited by 74 · see citing works
Schmitz, A., Fischer, S., Mattheyer, C., Pampaloni, F., & Stelzer, E. H. K. (2017) · Scientific Reports · doi:10.1038/srep43693 · Cited by 68 · see citing works
Smyrek, I., & Stelzer, E. H. K. (2017) · Biomedical Optics Express · doi:10.1364/boe.8.000484 · Cited by 62 · see citing works
Modeling Tumor Microenvironments In Vitro
Wu, M., & Swartz, M. A. (2014) · Journal of Biomechanical Engineering · doi:10.1115/1.4026447 · Cited by 60 · see citing works
Clarifying intact 3D tissues on a microfluidic chip for high-throughput structural analysis
Chen, Y., Silva, P. N., Syed, A., Sindhwani, S., Rocheleau, J., & Chan, W. W. C. (2016) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1609569114 · Cited by 59 · see citing works
Klicks, J., Maßlo, C., Kluth, M. A., Rudolf, R., & Hafner, M. (2019) · BMC Cancer · doi:10.1186/s12885-019-5606-4 · Cited by 59 · see citing works
Self-citationA computational image analysis glossary for biologists
Roeder, A., Cunha, A., Burl, M. C., & Meyerowitz, E. M. (2012) · Development · doi:10.1242/dev.076414 · Cited by 57 · see citing works
Three-dimensional imaging and quantitative analysis in CLARITY processed breast cancer tissues
Chen, Y., Shen, Q., White, S. L. P., Gökmen‐Polar, Y., Badve, S., & Goodman, L. J. (2019) · Scientific Reports · doi:10.1038/s41598-019-41957-w · Cited by 55 · see citing works
Pathophysiologically relevant in vitro tumor models for drug screening
Das, V., Bruzzese, F., Konečný, P., Iannelli, F., Budillon, A., & Hajdúch, M. (2015) · Drug Discovery Today · doi:10.1016/j.drudis.2015.04.004 · Cited by 53 · see citing works
Quantitative assessment of optical clearing methods in various intact mouse organs
Xu, J., Ma, Y., Yu, T., & Zhu, D. Y. (2018) · Journal of Biophotonics · doi:10.1002/jbio.201800134 · Cited by 52 · see citing works
Impact of physical confinement on nuclei geometry and cell division dynamics in 3D spheroids
Desmaison, A., Guillaume, L., Triclin, S., Weiss, P. O., Ducommun, B., & Lobjois, V. (2018) · Scientific Reports · doi:10.1038/s41598-018-27060-6 · Cited by 50 · see citing works
High-resolution in-depth imaging of optically cleared thick samples using an adaptive SPIM
Masson, A., Escande, P., Frongia, C., Clouvel, G., Ducommun, B., & Lorenzo, C. (2015) · Scientific Reports · doi:10.1038/srep16898 · Cited by 46 · see citing works
Anti-Cancer Drug Validation: the Contribution of Tissue Engineered Models
Carvalho, M. R., Lima, D., Reis, R. L., Oliveira, J. M., & Correlo, V. M. (2017) · Stem Cell Reviews and Reports · doi:10.1007/s12015-017-9720-x · Cited by 44 · see citing works
Histologic evidence of periodontal regeneration in furcation defects: a systematic review
Laugisch, O., Cosgarea, R., Nikou, G., Nikolidakis, D., Donos, N., Salvi, G. E., Stavropoulos, A., Jepsen, S. V., & Sculean, A. (2019) · Clinical Oral Investigations · doi:10.1007/s00784-019-02964-3 · Cited by 39 · see citing works
Designing Drug‐Response Experiments and Quantifying their Results
Hafner, M. A., Niepel, M., Subramanian, K., & Sorger, P. K. (2017) · Current Protocols in Chemical Biology · doi:10.1002/cpch.19 · Cited by 38 · see citing works
Self-citationBossolani, G. D. P., Pintelon, I., Detrez, J. R., Buckinx, R., Thys, S., Zanoni, J. N., Vos, W. H. D., & Timmermans, J. (2019) · Neurogastroenterology & Motility · doi:10.1111/nmo.13560 · Cited by 38 · see citing works
Into the Depths: Techniques for in Vitro Three-Dimensional Microtissue Visualization
Kabadi, P. K., Vantangoli, M. M., Rodd, A. L., Leary, E., Madnick, S. J., Morgan, J. R., Kane, A. B., & Boekelheide, K. (2015) · BioTechniques · doi:10.2144/000114353 · Cited by 37 · see citing works
On-chip clearing of arrays of 3-D cell cultures and micro-tissues
Grist, S. M., Nasseri, S. S., Poon, T. K. C., Roskelley, C. D., & Cheung, K. C. (2016) · Biomicrofluidics · doi:10.1063/1.4959031 · Cited by 35 · see citing works
Quantitative confocal microscopy
Jonkman, J. E. N., Brown, C. M., & Cole, R. W. (2014) · Methods in cell biology · doi:10.1016/b978-0-12-420138-5.00007-0 · Cited by 34 · see citing works
Williams, M. P. I., Rigon, M., Straka, T., Hörner, S. J., Thiel, M., Gretz, N., Hafner, M., Reischl, M., & Rudolf, R. (2019) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2019.00049 · Cited by 34 · see citing works
Self-citationHochheimer, A., Krohn, M., Rudert, K., Riedel, K., Becker, S., Thirion, C., & Zinke, H. (2014) · Chemical Senses · doi:10.1093/chemse/bju009 · Cited by 33 · see citing works
Self-citationBerlanga, M. L., Phan, S., Bushong, E. A., Wu, S., Kwon, O., Phung, B. S., Lamont, S., Terada, M., Taşdizen, T., Martone, M. E., et al. (2011) · Frontiers in Neuroanatomy · doi:10.3389/fnana.2011.00017 · Cited by 32 · see citing works
The third dimension: new developments in cell culture models for colorectal research
Pereira, J. C., Awatade, N. T., Loureiro, C. A., Matos, P., Amaral, M. D., & Jordan, P. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2258-2 · Cited by 32 · see citing works
Tumor Organoids Fill the Niche
Shroyer, N. F. (2016) · Cell stem cell · doi:10.1016/j.stem.2016.05.020 · Cited by 32 · see citing works
Blin, G., Sadurska, D., Migueles, R. P., Chen, N., Watson, J. A., & Lowell, S. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000388 · Cited by 30 · see citing works
Röhe, I., Hüttner, F. J., Plendl, J., Drewes, B., & Zentek, J. (2018) · European Journal of Histochemistry · doi:10.4081/ejh.2018.2874 · Cited by 28 · see citing works
Diagnostic difficulties with the diagnosis of small cell carcinoma of the lung
Marchevsky, A. M., & Wick, M. R. (2015) · Seminars in Diagnostic Pathology · doi:10.1053/j.semdp.2015.11.001 · Cited by 26 · see citing works
Accuracy in Quantitative 3D Image Analysis
Bassel, G. W. (2015) · The Plant Cell · doi:10.1105/tpc.114.135061 · Cited by 21 · see citing works
Yu, T., Qi, Y., Wang, J., Feng, W., Xu, J., Zhu, J., Yao, Y., Gong, H., Luo, Q., & Zhu, D. Y. (2016) · Journal of Biomedical Optics · doi:10.1117/1.jbo.21.8.081203 · Cited by 21 · see citing works
Costa, E. C., Moreira, A. F., de Melo‐Diogo, D., & Correia, I. J. (2018) · Journal of Biomedical Optics · doi:10.1117/1.jbo.23.5.055003 · Cited by 18 · see citing works
da Costa, M. M., Alves, L. P., Osório, R. A. L., Pacheco, M. T. T., & Silveira, L. (2018) · Journal of Biomedical Optics · doi:10.1117/1.jbo.23.10.107003 · Cited by 18 · see citing works
Costa, E. C., Moreira, A. F., de Melo‐Diogo, D., & Correia, I. J. (2018) · Optics & Laser Technology · doi:10.1016/j.optlastec.2018.04.002 · Cited by 17 · see citing works
Relevance of in vitro 3-D skin models in dissecting cytokine contribution to psoriasis pathogenesis.
Chiricozzi, A., Romanelli, M., Panduri, S., Donetti, E., & Prignano, F. (2017) · PubMed · doi:10.14670/hh-11-877 · Cited by 16 · see citing works
Bauer, S., Huldt, C. W., Kanebratt, K. P., Durieux, I., Gunne, D., Andersson, S., Ewart, L. C., Haynes, W. G., Maschmeyer, I., Winter, A., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-20340-1 · Cited by 15 · see citing works
Chen, Y., Tsai, Y., Liu, Y.-A., Lee, S.-H., Tseng, S., & Tang, S. (2013) · The Scientific World JOURNAL · doi:10.1155/2013/624342 · Cited by 14 · see citing works
Immunostaining of Skeletal Tissues
Kurth, T. B., & Bari, C. D. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-415-5_21 · Cited by 9 · see citing works
Immunostaining of Skeletal Tissues
Roelofs, A. J., & Bari, C. D. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-8997-3_25 · Cited by 7 · see citing works
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Pinto, B., Henriques, A. C., Silva, P. M. A., & Bousbaa, H. (2020) · Pharmaceutics · doi:10.3390/pharmaceutics12121186 · Cited by 440 · see citing works
3D cell cultures toward quantitative high-throughput drug screening
Wang, Y., & Jeon, H. (2022) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2022.03.014 · Cited by 143 · see citing works
Fluorescence Microscopy—An Outline of Hardware, Biological Handling, and Fluorophore Considerations
Hickey, S. M., Ung, B. S. ‐., Bader, C. A., Brooks, R. D., Łaźniewska, J., Johnson, I. R. D., Sorvina, A., Logan, J. M., Martini, C., Moore, C. R., et al. (2021) · Cells · doi:10.3390/cells11010035 · Cited by 144 · see citing works
Rigor and reproducibility in human brain organoid research: Where we are and where we need to go
Sandoval, S. O., Cappuccio, G., Kruth, K., Osenberg, S., Khalil, S. M., Méndez-Albelo, N. M., Padmanabhan, K., Wang, D., Niciu, M. J., Bhattacharyya, A., et al. (2024) · Stem Cell Reports · doi:10.1016/j.stemcr.2024.04.008 · Cited by 79 · see citing works
Pamies, D., Ekert, J., Zurich, M.-G., Frey, O., Werner, S., Piergiovanni, M., Freedman, B. S., Keong Teo, A. K., Erfurth, H., Reyes, D. R., et al. (2024) · Stem Cell Reports · doi:10.1016/j.stemcr.2024.03.009 · Cited by 66 · see citing works
Assay establishment and validation of a high-throughput organoid-based drug screening platform
Li, X., Fu, G., Zhang, L., Guan, R., Tang, P., Zhang, J., Rao, X., Chen, S., Xu, X., Zhou, Y., et al. (2022) · Stem Cell Research & Therapy · doi:10.1186/s13287-022-02902-3 · Cited by 56 · see citing works
Bang, S., Lee, S., Choi, N., & Kim, H. N. (2021) · Advanced Healthcare Materials · doi:10.1002/adhm.202002119 · Cited by 55 · see citing works
Development of a deep learning based image processing tool for enhanced organoid analysis
Park, T., Kim, T. K., Han, Y. D., Kim, K., Kim, H., & Kim, H. S. (2023) · Scientific Reports · doi:10.1038/s41598-023-46485-2 · Cited by 51 · see citing works
Recent Trends and Perspectives in Cerebral Organoids Imaging and Analysis
Martin, C. B., Simon-Chane, C., Clouchoux, C., & Histace, A. (2021) · Frontiers in Neuroscience · doi:10.3389/fnins.2021.629067 · Cited by 41 · see citing works
Morsby, J. J., Zhang, Z., Burchett, A. A., Datta, M., & Smith, B. D. (2024) · Chemical Science · doi:10.1039/d3sc06058f · Cited by 36 · see citing works
Optical tissue clearing associated with 3D imaging: application in preclinical and clinical studies
Brenna, C., Simioni, C., Varano, G., Conti, I., Costanzi, E., Melloni, M., & Neri, L. M. (2022) · Histochemistry and Cell Biology · doi:10.1007/s00418-022-02081-5 · Cited by 34 · see citing works
Goodarzi, S., Prunet, A., Rossetti, F., Bort, G., Tillement, O., Porcel, E., Lacombe, S., Wu, T.-D., Guerquin-Kern, J.-L., Delanoë-Ayari, H., et al. (2021) · Lab on a Chip · doi:10.1039/d1lc00192b · Cited by 29 · see citing works
Perspective: Extending the Utility of Three-Dimensional Organoids by Tissue Clearing Technologies
Susaki, E. A., & Takasato, M. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.679226 · Cited by 26 · see citing works
Yasuhiko, O., & Takeuchi, K. (2023) · Light Science & Applications · doi:10.1038/s41377-023-01144-z · Cited by 27 · see citing works
Factors to consider when interrogating 3D culture models with plate readers or automated microscopes
Riss, T., & Trask, O. J. (2021) · In Vitro Cellular & Developmental Biology - Animal · doi:10.1007/s11626-020-00537-3 · Cited by 26 · see citing works
A Scaffold-Free 3-D Co-Culture Mimics the Major Features of the Reverse Warburg Effect In Vitro
Keller, F., Bruch, R., Schneider, R., Meier-Hubberten, J. C., Hafner, M., & Rudolf, R. (2020) · Cells · doi:10.3390/cells9081900 · Cited by 24 · see citing works
Self-citationTurrini, E., Ulfo, L., Costantini, P. E., Saporetti, R., Giosia, M. D., Nigro, M., Petrosino, A., Pappagallo, L., Kaltenbrunner, A., Cantelli, A., et al. (2024) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-024-05174-7 · Cited by 21 · see citing works
Hiramoto, K., Komatsu, K., Shikuwa, R., Konno, A., Sato, Y., Hirano‐Iwata, A., Ino, K., & Shiku, H. (2023) · Electrochimica Acta · doi:10.1016/j.electacta.2023.142507 · Cited by 20 · see citing works
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Schäfer, M. E. A., Keller, F., Schumacher, J., Haas, H., Vascotto, F., Şahin, U., Hafner, M., & Rudolf, R. (2022) · Cells · doi:10.3390/cells11061026 · Cited by 18 · see citing works
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Chen, C., Peng, S.-J., Chou, Y.-H., Lee, C., Lee, P., Hu, R., Ho, M., Chung, M., Hsiao, F.-T., Tien, Y., et al. (2024) · American Journal of Physiology-Endocrinology and Metabolism · doi:10.1152/ajpendo.00205.2023 · Cited by 19 · see citing works
The Evolution of Technology‐Driven In Vitro Models for Neurodegenerative Diseases
Vitis, E. D., Stanzione, A., Romano, A., Quattrini, A., Gigli, G., Moroni, L., Gervaso, F., & Polini, A. (2024) · Advanced Science · doi:10.1002/advs.202304989 · Cited by 16 · see citing works
Sensing Senses: Optical Biosensors to Study Gustation
von Molitor, E., Riedel, K., Hafner, M., Rudolf, R., & Cesetti, T. (2020) · Sensors · doi:10.3390/s20071811 · Cited by 17 · see citing works
Self-citationTartagni, O., Borók, A., Mensa’, E., Bonyár, A., Monti, B., Hofkens, J., Porcelli, A. M., & Zuccheri, G. (2023) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-023-04748-1 · Cited by 16 · see citing works
Vitacolonna, M., Bruch, R., Schneider, R., Jabs, J., Hafner, M., Reischl, M., & Rudolf, R. (2024) · BMC Cancer · doi:10.1186/s12885-024-13329-9 · Cited by 15 · see citing works
Self-citationDiósdi, Á., Hirling, D., Kovács, M., Tóth, T., Harmati, M., Koós, K., Buzás, K., Piccinini, F., & Horváth, P. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.01.040 · Cited by 13 · see citing works
In-silico and in-vitro morphometric analysis of intestinal organoids
Montes-Olivas, S., Legge, D., Lund, A., Fletcher, A. G., Williams, A. C., Marucci, L., & Homer, M. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011386 · Cited by 16 · see citing works
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Amado, B., Melo, L., Pinto, R., Lobo, A. C., Barros, P., & Gomes, J. R. (2022) · Biomedicines · doi:10.3390/biomedicines10102561 · Cited by 14 · see citing works
SpheroScan: a user-friendly deep learning tool for spheroid image analysis
Akshay, A., Katoch, M., Abedi, M., Shekarchizadeh, N., Besic, M., Burkhard, F. C., Bigger-Allen, A., Adam, R. M., Monastyrskaya, K., & Gheinani, A. H. (2022) · GigaScience · doi:10.1093/gigascience/giad082 · Cited by 14 · see citing works
Olofsson, K., Carannante, V., Takai, M., Önfelt, B., & Wiklund, M. (2021) · Scientific Reports · doi:10.1038/s41598-021-96288-6 · Cited by 13 · see citing works
Flörkemeier, I., Hillmann, J. S., Weimer, J. P., Hildebrandt, J., Hedemann, N., Rogmans, C., Dempfle, A., Arnold, N., Clement, B., & Bauerschlag, D. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms231810503 · Cited by 13 · see citing works
Protocol for the generation and automated confocal imaging of whole multi-cellular tumor spheroids
Genenger, B., McAlary, L., Perry, J. R., Ashford, B., & Ranson, M. (2023) · STAR Protocols · doi:10.1016/j.xpro.2023.102331 · Cited by 13 · see citing works
Kelly, S., Byrne, M. H., Quinn, S. J., & Simpson, J. C. (2021) · Nanoscale · doi:10.1039/d1nr04460e · Cited by 13 · see citing works
Multiscale Analysis of Cellular Composition and Morphology in Intact Cerebral Organoids
Ma, H., Chen, J., Deng, Z., Sun, T., Luo, Q., Gong, H., Li, X., & Long, B. (2022) · Biology · doi:10.3390/biology11091270 · Cited by 14 · see citing works
Fluid preservation in brain banking: a review
McKenzie, A. T., Nnadi, O., Slagell, K. D., Thorn, E. L., Farrell, K. W., & Crary, J. F. (2024) · Free Neuropathology · doi:10.17879/freeneuropathology-2024-5373 · Cited by 11 · see citing works
Navigating across multi-dimensional space of tissue clearing parameters
Avilov, S. (2021) · Methods and Applications in Fluorescence · doi:10.1088/2050-6120/abe6fb · Cited by 10 · see citing works
Mahmoud, L., Cougnoux, A., Bekiari, C., teba, P. A. R. D. C., Marrahi, A. E., panneau, G., Gsell, L., & Hausser, J. (2023) · Experimental Cell Research · doi:10.1016/j.yexcr.2023.113527 · Cited by 9 · see citing works
Ahmad, A., Goodarzi, S., Frindel, C., Recher, G., Rivière, C., & Rousseau, D. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.31.428996 · Cited by 10 · see citing works
Zhang, Z., Sanders, H. S., Dragun, V., Cole, S. L., & Smith, B. D. (2025) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.4c22228 · Cited by 9 · see citing works
Synthesis of large scale 3D microscopic images of 3D cell cultures for training and benchmarking
Bruch, R., Keller, F., Böhland, M., Vitacolonna, M., Klinger, L., Rudolf, R., & Reischl, M. (2023) · PLoS ONE · doi:10.1371/journal.pone.0283828 · Cited by 9 · see citing works
Self-citationOh, M.-S., Khawar, I. A., Lee, D. W., Park, J. K., & Kuh, H. (2020) · Cancers · doi:10.3390/cancers12123662 · Cited by 9 · see citing works
MSLASpheroidStamp: 3d cell spheroids for everyone
Минин, А. С., Semerikova, T., Belousova, A. V., Karavashkova, O., Pozdina, V. A., Tomilina, M., & Zubarev, I. V. (2025) · Bioprinting · doi:10.1016/j.bprint.2025.e00416 · Cited by 8 · see citing works
Schäfer, M. E. A., Klicks, J., Hafner, M., & Rudolf, R. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1205-7_13 · Cited by 7 · see citing works
Self-citation3D models of the dynamics of cancer cells under external pressure
Игоревна, С. Н., & Tuchin, V. V. (2021) · Chaos An Interdisciplinary Journal of Nonlinear Science · doi:10.1063/5.0056764 · Cited by 8 · see citing works
Thanh, M. T. H., Poudel, A., Ameen, S., Carroll, B., Wu, M., Soman, P., Zhang, T., Schwarz, J. M., & Patteson, A. E. (2026) · Communications Biology · doi:10.1038/s42003-026-10506-3 · Cited by 7 · see citing works
On-chip clearing for live imaging of 3D cell cultures
Yu, T., Zhong, X., Yang, Q., Gao, C., Chen, W., Liu, X., Liu, Z., Zhu, T., Li, D., Fei, P., et al. (2023) · Biomedical Optics Express · doi:10.1364/boe.489219 · Cited by 7 · see citing works
Transparent tissue in solid state for solvent-free and antifade 3D imaging
Hsiao, F.-T., Chien, H., Chou, Y.-H., Peng, S.-J., Chung, M., Huang, T.-H., Lo, L.-W., Shen, C., Chang, H.-P., Lee, C., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39082-4 · Cited by 6 · see citing works
Komen, J., van Neerven, S. M., Bossink, E. G. B. M., de Groot, N. E., Nijman, L. E., van den Berg, A., Vermeulen, L., & van der Meer, A. D. (2022) · Micromachines · doi:10.3390/mi13050739 · Cited by 6 · see citing works
Droplet contact-based spheroid transfer technique as a multi-step assay tool for spheroid arrays
Kim, H., Roh, H., Kim, H., & Park, J. (2021) · Lab on a Chip · doi:10.1039/d1lc00581b · Cited by 6 · see citing works
Marozin, S., Simon‐Nobbe, B., Huth, A., Beyerer, E., Weber, L., Nussler, A. K., & Lepperdinger, G. (2024) · Scientific Reports · doi:10.1038/s41598-024-60986-8 · Cited by 5 · see citing works
Nürnberg, E., Vitacolonna, M., Bruch, R., Reischl, M., Rudolf, R., & Sauer, S. (2024) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2024.1467366 · Cited by 5 · see citing works
Self-citationAnameriç, A., Czerwonka, A., & Nees, M. (2023) · Cancers · doi:10.3390/cancers15225320 · Cited by 5 · see citing works
Magnetic 3D bioprinting of skeletal muscle spheroid for a spheroid-based screening assay
Chaweewannakorn, C., Aye, K. T. N., & Ferreira, J. N. (2024) · SLAS DISCOVERY · doi:10.1016/j.slasd.2024.100190 · Cited by 5 · see citing works
High-content morphological profiling by Cell Painting in 3D spheroidsPreprint
Ringers, C., Holmberg, D., Flobak, Å., Georgieva, P., Jarvius, M., Johansson, M. M., Larsson, A. O., Rosén, D., Seashore-Ludlow, B. A., Visnes, T., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.05.636642 · Cited by 5 · see citing works
Predicting nanocarriers’ efficacy in 3D models with Brillouin microscopy
Guerriero, G., Viel, A., Feltri, V., Balboni, A., Yan, G., Monnier, S., Lollo, G., & Dehoux, T. (2023) · Nanoscale · doi:10.1039/d3nr03502f · Cited by 4 · see citing works
Evaluating cell growth and hypoxic regions of 3D spheroids via a machine learning approach
Yoo, J., Choi, J. W., Kim, E., Park, E., Baek, A., Kim, J., Jeong, M. S., Cho, Y., Lee, T. G., & Heo, M. B. (2024) · Machine Learning Science and Technology · doi:10.1088/2632-2153/ad718e · Cited by 4 · see citing works
Efficient wet-spinning of pre-aligned microtissues for 3D bioprinting complex tissue alignment
Vogt, C. D., Broomhead, J. R., Kunisaki, K. Y., Teegarden, J. M., Frett, K. L., Pacello, K. Q., Vitale, A. H., & Panoskaltsis‐Mortari, A. (2025) · Biofabrication · doi:10.1088/1758-5090/add37f · Cited by 5 · see citing works
Keller, F., Bruch, R., Clauder, F., Hafner, M., & Rudolf, R. (2021) · Cells · doi:10.3390/cells10061304 · Cited by 4 · see citing works
Self-citationRapid Optical Clearing for High-Throughput Analysis of Tumour SpheroidsPreprint
Gunasingh, G. P., Browning, A. P., & Haass, N. K. (2021) · Preprints.org · doi:10.20944/preprints202111.0488.v1 · Cited by 4 · see citing works
Establishment of a three‑dimensional triculture model on the novel AXTEX‑4D™ platform
Baru, A., Mazumder, S., Kundu, P. K., Sharma, S., Purakayastha, B. P. D., Khan, S. M., Gupta, R., & Arora, N. M. (2022) · Oncology Reports · doi:10.3892/or.2022.8439 · Cited by 3 · see citing works
Conditions of acceleration and deceleration of the cancer cell growth under osmotic pressure
Svetlitsyna, N. A., Игоревна, С. Н., & Tuchin, V. V. (2024) · Chaos An Interdisciplinary Journal of Nonlinear Science · doi:10.1063/5.0189550 · Cited by 3 · see citing works
Phenotypic analysis of complex bioengineered 3D models
Ravichandran, A., Mahajan, V., van de Kemp, T., Taubenberger, A. V., & Bray, L. J. (2025) · Trends in Cell Biology · doi:10.1016/j.tcb.2024.12.004 · Cited by 3 · see citing works
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Zillich, L., Gasparotto, M., Rossetti, A. C., Fechtner, O., Maillard, C., Hoffrichter, A., Zillich, E., Jabali, A., Marsoner, F., Artioli, A., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.19.520907 · Cited by 3 · see citing works
Tariq, A., Naz, I., Arshad, F., Chinnappan, R., Mir, T. A., Khan, M. I., & Yaqinuddin, A. (2026) · Biosensors · doi:10.3390/bios16040188 · Cited by 2 · see citing works
Rapid Optical Clearing for Semi-High-Throughput Analysis of Tumor Spheroids
Gunasingh, G. P., Browning, A. P., & Haass, N. K. (2022) · Journal of Visualized Experiments · doi:10.3791/64103 · Cited by 2 · see citing works
Santos, M. C. D. L., & Lundqvist, A. (2024) · Methods in cell biology · doi:10.1016/bs.mcb.2024.10.015 · Cited by 1 · see citing works
Lin, C.-H., Leng, Z.-C., Yu, C.-H., Bharali, L. K. D., Lin, C., Mao, B.-H., & Tu, T. (2025) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2025.109761 · Cited by 1 · see citing works
ClearAIM: dynamic quantitative label-free monitoring of tissue optical clearing
Kalinowski, K., Chwastowicz, A., Arcab, P., Rogalski, M., Szymska, W., Wdowiak, E., Winnik, J., Zdańkowski, P., Jóźwik, M., Matryba, P., et al. (2025) · Advanced imaging. · doi:10.3788/ai.2025.10022 · Cited by 1 · see citing works
Use of bovine serum albumin might impair immunofluorescence signal in thick tissue samples
Chwastowicz, A., Wolny, A., Sobień, M., Barański, M., Tomczuk, J., Szatkowski, M., Szredzka, A., Gołąb, J., Kaczmarek, L., Stefaniuk, M., et al. (2025) · Scientific Reports · doi:10.1038/s41598-025-06876-z · Cited by 1 · see citing works
Development of a laser injury model using human cardiac spheroids
Adak, A., Strasser, R., Meer, M., Arora, P., Osterwalder, M., Mercader, N., & Zuppinger, C. (2026) · Disease Models & Mechanisms · doi:10.1242/dmm.052855 · Cited by 1 · see citing works
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Nürnberg, E., Bruch, R., Hafner, M., Rudolf, R., & Vitacolonna, M. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-3674-9_20 · Cited by 1 · see citing works
Self-citationRapid Optical Clearing for High-Throughput Analysis of Tumour SpheroidsPreprint
Gunasingh, G. P., Browning, A. P., & Haass, N. K. (2022) · Preprints.org · doi:10.20944/preprints202111.0488.v2 · Cited by 1 · see citing works
Mahmoud, L., Cougnoux, A., Bekiari, C., teba, P. A. R. D. C., Marrahi, A. E., panneau, G., Gsell, L., & Hausser, J. (2022) · Research Square · doi:10.21203/rs.3.rs-2279201/v1
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Montes-Olivas, S., Legge, D., Lund, A., Fletcher, A. G., Williams, A. C., Marucci, L., & Homer, M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.08.519603
Rapid Optical Clearing for Semi-High-Throughput Analysis of Tumor Spheroids
Gunasingh, G. P., Browning, A. P., & Haass, N. K. (2022) · Journal of Visualized Experiments · doi:10.3791/64103-v
Svetlitsyna, N. A., Tuchin, V. V., & Игоревна, С. Н. (2024) · Izvestiya of Saratov University Physics · doi:10.18500/1817-3020-2024-24-4-374-383
Cui, W., Haffa, M., Massai, F., Qian, K., Vallin, M., Axelsson, H., & Seashore-Ludlow, B. A. (2025) · Royal Society of Chemistry eBooks · doi:10.1039/9781837676941-00168
Saberigarakani, A., Brewer, J., & Ding, Y. (2025) · Current Treatment Options in Cardiovascular Medicine · doi:10.1007/s11936-025-01105-2
Anameriç, A., Reszczyńska, E., Stankiewicz, T., Andrzejczak, A., Stepulak, A., & Nees, M. (2025) · Cells · doi:10.3390/cells14191543
Kim, K., Singla, R., Chaware, A., Park, J., Klockner, I., Lerner, J. F., Li, K., Shen, F., Dugo, C., Reamey, P., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.07.681020
Li, X., Fu, G., Zhang, L., Guan, R., Tang, P., Zhang, J., Rao, X., Chen, S., Xu, X., Zhou, Y., et al. (2022) · Figshare · doi:10.6084/m9.figshare.19906792
Cesetti, T., Buerger, C., Couturier, N., Nürnberg, E., Bruch, R., Lang, V., Hafner, M., Reischl, M., Fauth, T., & Rudolf, R. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.21.700040
Self-citationQuantifying single-cell responses to irradiation in 3D
François, J., Simerzin, A., Jambhekar, A., & Lahav, G. (2026) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2026.1735308
Martin, C. B. (2023) · theses.fr (ABES) · doi:10.70675/8eea9293zdaadz4766z9baez15cec27b3b07
In Vitro Models of Neurodegenerative Diseases
Saleh, A., & Becker, E. B. E. (2026) · Contemporary clinical neuroscience · doi:10.1007/978-3-032-18296-8_6
Cesetti, T., Buerger, C., Couturier, N., Nürnberg, E., Bruch, R., Vitacolonna, M., Lang, V., Hafner, M., Reischl, M., Fauth, T., et al. (2026) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2026.1887652
Self-citationParallelized bright-field and fluorescence imaging platform for organoids
Kim, K., Singla, R., Chaware, A., Park, J., Klockner, I., Lerner, J. F., Li, K., Shen, F., Dugo, C., Reamey, P., et al. (2026) · Cell Reports Methods · doi:10.1016/j.crmeth.2026.101601
Fomina, A., Tam, A., Lam, J., Wu, N. C., Li, N. T., & McGuigan, A. P. (2026) · Advanced Materials Technologies · doi:10.1002/admt.71311
Lu, T., Muntean, C., Sauvage, F., Punj, D., Keersmaecker, H. D., Baeke, F., Rycke, R. M. D., Lemeire, K., Tummers, P., Li, W., et al. (2026) · Science Advances · doi:10.1126/sciadv.aeh0675
Machine learning-based brightfield detection of anti-fibrotic effects in a 3D retinal fibrosis model
Hofstetter, T., Grining, Ö. Y., Roubeix, C., Westenskow, P. D., & Fluri, D. A. (2026) · SLAS DISCOVERY · doi:10.1016/j.slasd.2026.100343
High-content morphological profiling by Cell Painting in 3D spheroids
Ringers, C., Holmberg, D., Larsson, A., Jung, B., Jarvius, M., Łuchniak, A., Rosén, D., Johansson, M., Georgiev, P., Seashore-Ludlow, B. A., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-78596-5 · Cited by 5 · see citing works
Astigiano, C., Lori, L., Euro, L., Caffa, I., Ghanem, M., Verzola, D., Ferrera, F., Fenoglio, D., Passalacqua, M., Grozio, A., et al. (2026) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2026.120006
Lipoplex Nanoparticle-Based RNA Delivery to 3D Melanoma Spheroids
Rudolf, R., Cesetti, T., Keller, F., & Hafner, M. (2026) · Methods in molecular biology · doi:10.1007/978-1-0716-5619-8_37
Self-citation
- Authors
- Nürnberg, E., Vitacolonna, M., Klicks, J., von Molitor, E., Cesetti, T., Keller, F., Bruch, R., Ertongur-Fauth, T., Riedel, K., Scholz, P., Lau, T., Schneider, R., Meier, J., Hafner, M., & Rudolf, R.
- Affiliations
- Heidelberg University (DE)
- Merck KGaA, Darmstadt (Germany) (DE)
- Corresponding author
- Rudolf, Rüdiger
- ORCID
- Venue
- Frontiers in Molecular Biosciences
- Publisher
- Frontiers Media SA
- Published
- 2020-02-21
- Volume
- 7
- Pages
- 20-20
- ISSN
- 2296-889X (ISSN-L)
- PMC
- PMC7046628
- OpenAlex
- W3008097711
- Cited by
- 93
- References
- 82
- Citations by year
- 2026: 14 · 2025: 12 · 2024: 16 · 2023: 13 · 2022: 18 · 2021: 16 · 2020: 4
- FWCI
- 6.07
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Molecular Biosciences (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Bundesministerium für Bildung und Forschung
- Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg
- Carl-Zeiss-Stiftung
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
- Physical Sciences › Engineering › Biomedical Engineering › 3D Printing in Biomedical Research
- Keywords
- optical tissue clearing, 3D cell culture, spheroids, organoids, sample shrinkage, signal-to-noise ratio, image segmentation, cell counting, co-culture, drug screening
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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