Researching | ClearAIM: dynamic quantitative label-free monitoring of tissue optical clearing

Journals >Advanced Imaging >Volume 2 >Issue 2 >Page 021003 > Article

Advanced Imaging
Vol. 2, Issue 2, 021003 (2025)

ClearAIM: dynamic quantitative label-free monitoring of tissue optical clearing | Editors' Pick

Kamil Kalinowski^1,†, Anna Chwastowicz^2,3, Piotr Arcab¹, Mikołaj Rogalski¹..., Wiktoria Szymska¹, Emilia Wdowiak¹, Julianna Winnik¹, Piotr Zdańkowski¹, Michał Józwik¹, Paweł Matryba^2,3,4,* and Maciej Trusiak^1,*|Show fewer author(s)

Author Affiliations

¹Institute of Micromechanics and Photonics, Faculty of Mechatronics, Warsaw University of Technology, Warsaw, Poland

²Department of Immunology, Medical University of Warsaw, Warsaw, Poland

³Laboratory of Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland

⁴Department of Radiology 1, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland

show less

DOI: 10.3788/AI.2025.10022 Cite this Article Set citation alerts

Kamil Kalinowski, Anna Chwastowicz, Piotr Arcab, Mikołaj Rogalski, Wiktoria Szymska, Emilia Wdowiak, Julianna Winnik, Piotr Zdańkowski, Michał Józwik, Paweł Matryba, Maciej Trusiak, "ClearAIM: dynamic quantitative label-free monitoring of tissue optical clearing," Adv. Imaging 2, 021003 (2025) Copy Citation Text

show less

References

[1] P. Matryba, L. Kaczmarek, J. Gołąb. Advances in ex situ tissue optical clearing. Laser Photonics Rev., 13, 1800292(2019). https://doi.org/10.1002/lpor.201800292

[2] I. Costantini et al. In-vivo and ex-vivo optical clearing methods for biological tissues: review. Biomed. Opt. Express, 10, 5251(2019). https://doi.org/10.1364/BOE.10.005251

[3] H. Mai, D. Lu. Tissue clearing and its applications in human tissues: a review. VIEW, 5, 20230046(2024). https://doi.org/10.1002/VIW.20230046

[4] O. Zihao et al. Achieving optical transparency in live animals with absorbing molecules. Science, 385, eadm6869(2024). https://doi.org/10.1126/science.adm6869

[5] M. V. Gómez-Gaviro et al. Biomedical applications of tissue clearing and three-dimensional imaging in health and disease. iScience, 23, 101432(2020). https://doi.org/10.1016/j.isci.2020.101432

[6] K. Tainaka et al. Chemical landscape for tissue clearing based on hydrophilic reagents. Cell Rep., 24, 2196(2018). https://doi.org/10.1016/j.celrep.2018.07.056

[7] D. Kurihara et al. ClearSeeAlpha: advanced optical clearing for whole-plant imaging. Plant Cell Physiol., 62, 1302(2021). https://doi.org/10.1093/pcp/pcab033

[8] W. Li, R. N. Germain, M. Y. Gerner. High-dimensional cell-level analysis of tissues with Ce3D multiplex volume imaging. Nat. Protoc., 14, 1708(2019). https://doi.org/10.1038/s41596-019-0156-4

[9] G. D. P. Bossolani et al. Comparative analysis reveals Ce3D as optimal clearing method for in toto imaging of the mouse intestine. Neurogastroenterol. Motil., 31, e13560(2019). https://doi.org/10.1111/nmo.13560

[10] A. Azaripour et al. A survey of clearing techniques for 3D imaging of tissues with special reference to connective tissue. Prog. Histochem. Cytochem., 51, 9(2016). https://doi.org/10.1016/j.proghi.2016.04.001

[11] P. Matryba et al. Systematic evaluation of chemically distinct tissue optical clearing techniques in murine lymph nodes. J. Immunol., 204, 1395(2020). https://doi.org/10.4049/jimmunol.1900847

[12] J. Xu et al. Quantitative assessment of optical clearing methods in various intact mouse organs. J. Biophotonics, 12, e201800134(2019). https://doi.org/10.1002/jbio.201800134

[13] Y. Schega, N. Flinner, M.-L. Hansmann. Quantitative assessment of optical clearing methods on formalin-fixed human lymphoid tissue. Pathol. Res. Pract., 216, 153136(2020). https://doi.org/10.1016/j.prp.2020.153136

[14] H. Rusch et al. Finding the best clearing approach - towards 3D wide-scale multimodal imaging of aged human brain tissue. NeuroImage, 247, 118832(2022). https://doi.org/10.1016/j.neuroimage.2021.118832

[15] M. Scardigli et al. Comparison of different tissue clearing methods for three-dimensional reconstruction of human brain cellular anatomy using advanced imaging techniques. Front. Neuroanat., 15, 123(2021). https://doi.org/10.3389/fnana.2021.752234

[16] D. Jing et al. Tissue clearing and its application to bone and dental tissues. J. Dent. Res., 98, 621(2019). https://doi.org/10.1177/0022034519844510

[17] J. Woo et al. Comparative analyses of clearing efficacies of tissue clearing protocols by using a punching assisted clarity analysis. Front. Bioeng. Biotechnol., 9, 784626(2022). https://doi.org/10.3389/fbioe.2021.784626

[18] J. H. Kim et al. Optimizing tissue-clearing conditions based on analysis of the critical factors affecting tissue-clearing procedures. Sci. Rep., 8, 12815(2018). https://doi.org/10.1038/s41598-018-31153-7

[19] A. Kirillov et al. Segment anything(2023).

[20] K. J. Kalinowski. ClearAIM project(2023). https://github.com/kamil-janusz-kalinowski/ClearAIM.git

[21] E. A. Susaki et al. Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Cell, 157, 726(2014). https://doi.org/10.1016/j.cell.2014.03.042

[22] E. Nürnberg et al. Routine optical clearing of 3D-cell cultures: simplicity forward. Front. Mol. Biosci., 7, 1(2020). https://doi.org/10.3389/fmolb.2020.00001

[23] P. Matryba et al. Optimized perfusion-based CUBIC protocol for the efficient whole-body clearing and imaging of rat organs. J. Biophotonics, 11, e201700248(2017). https://doi.org/10.1002/jbio.201700248

[24] J. Xie et al. Morphological analysis of descending tracts in mouse spinal cord using tissue clearing, tissue expansion and tiling light sheet microscopy techniques. Sci. Rep., 13, 16445(2023). https://doi.org/10.1038/s41598-023-43610-z

[25] C. Pan et al. Shrinkage-mediated imaging of entire organs and organisms using uDISCO. Nat. Methods, 13, 859(2016). https://doi.org/10.1038/nmeth.3964

[26] X. Zhu et al. Ultrafast optical clearing method for three-dimensional imaging with cellular resolution. PNAS, 116, 11480(2019). https://doi.org/10.1073/pnas.1819583116

[27] Q.-H. Shan et al. A method for ultrafast tissue clearing that preserves fluorescence for multimodal and longitudinal brain imaging. BMC Biol., 20, 77(2020). https://doi.org/10.1186/s12915-022-01275-6

[28] P. Matryba et al. Tissue optical clearing and expanding solution for improved nuclear segmentation. VIEW, 6, 20240063(2025). https://doi.org/10.1002/VIW.20240063

Figures&Tables (5)

References (28)

Copy Citation Text

Kamil Kalinowski, Anna Chwastowicz, Piotr Arcab, Mikołaj Rogalski, Wiktoria Szymska, Emilia Wdowiak, Julianna Winnik, Piotr Zdańkowski, Michał Józwik, Paweł Matryba, Maciej Trusiak, "ClearAIM: dynamic quantitative label-free monitoring of tissue optical clearing," Adv. Imaging 2, 021003 (2025)

Download Citation

Set citation alerts for the article

Set citation alerts for the article

Save the article for my favorites

Paper Information

Recommended Topics

laser devices and laser physics

Lasers and Laser Optics

laser manufacturing

Instrumentation, Measurement and Metrology

Set citation alerts for the article

Please enter your email address