Skip to main content
Springer Nature Link
Log in

Software for Full-Color 3D Reconstruction of the Biological Tissues Internal Structure

  • Conference paper
  • First Online:
Health Information Science (HIS 2017)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 10594))

Included in the following conference series:

Abstract

A software for processing sets of full-color images of biological tissue histological sections is developed. We used histological sections obtained by the method of high-precision layer-by-layer grinding of frozen biological tissues. The software allows restoring the image of the tissue for an arbitrary cross-section of the tissue sample. Thus, our method is designed to create a full-color 3D reconstruction of the biological tissue structure. The resolution of 3D reconstruction is determined by the quality of the initial histological sections. The newly developed technology available to us provides a resolution of up to 5–10 μm in three dimensions.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Azinfar, L., Ravanfar, M., Wang, Y., Zhang, K., Duan, D., Yao, G.: High resolution imaging of the fibrous microstructure in bovine common carotid artery using optical polarization tractography. J. Biophotonics 10, 231–241 (2017). doi:10.1002/jbio.201500229

    Article  Google Scholar 

  2. Bobroff, V., Chen, H.-H., Delugin, M., Javerzat, S., Petibois, C.: Quantitative IR microscopy and spectromics open the way to 3D digital pathology. J. Biophotonics 10, 598–606 (2017). doi:10.1002/jbio.201600051

    Article  Google Scholar 

  3. Brazina, D., Fojtik, R., Rombova, Z.: 3D visualization in teaching anatomy. Procedia Soc. Behav. Sci. 143, 367–371 (2014). doi:10.1016/j.sbspro.2014.07.496

    Article  Google Scholar 

  4. Candemir, S., Jaeger, S., Antani, S., Bagci, U., Folio, L.R., Xu, Z., Thoma, G.: Atlas-based rib-bone detection in chest X-rays. Comput. Med. Imaging Graph. 51, 32–39 (2016). doi:10.1016/j.compmedimag.2016.04.002

    Article  Google Scholar 

  5. Cerveri, P., Manzotti, A., Confalonieri, N., Baroni, G.: Automating the design of resection guides specific to patient anatomy in knee replacement surgery by enhanced 3D curvature and surface modeling of distal femur shape models. Comput. Med. Imaging Graph. 38(8), 664–674 (2014). doi:10.1016/j.compmedimag.2014.09.001

    Article  Google Scholar 

  6. Chen, Y., Wang, Z., Li, L., Wan, X., Sun, F., Zhang, F.: A fully automatic geometric parameters determining method for electron tomography. In: Cai, Z., Daescu, O., Li, M. (eds.) ISBRA 2017. LNCS, vol. 10330, pp. 385–389. Springer, Cham (2017). doi:10.1007/978-3-319-59575-7_39

    Chapter  Google Scholar 

  7. Chiorean, L.D., Szasz, T., Vaida, M.F., Voina, A.: 3D reconstruction and volume computing in medical imaging. Acta Technica Napocensis 52(3), 18–24 (2011)

    Google Scholar 

  8. Cuijpers, V.M.J.I., Walboomers, X.F., Jansen, J.A.: Three-dimensional localization of implanted biomaterials in anatomical and histological specimens using combined x-ray computed tomography and three-dimensional surface reconstruction: a technical note. Tissue Eng. Part C Methods 16, 63–69 (2010). doi:10.1089/ten.TEC.2008.0604

    Article  Google Scholar 

  9. Ermilov, S.A., Su, R., Conjusteau, A., Anis, F., Nadvoretskiy, V., Anastasio, M.A., Oraevsky, A.A.: Three-dimensional optoacoustic and laser-induced ultrasound tomography system for preclinical research in mice: design and phantom validation. Ultrason. Imaging 38, 77–95 (2016). doi:10.1177/0161734615591163

    Article  Google Scholar 

  10. Ha, J.F., Morrison, R.J., Green, G.E., Zopf, D.A.: Computer-aided design and 3-dimensional printing for costal cartilage simulation of airway graft carving. Otolaryngol. Head Neck Surg. 1–4 (2017). doi:10.1177/0194599817697048

  11. Hanney, M.B., Hillel, P.G., Scott, A.D., Lorenz, E.: Half-body single photon emission computed tomography with resolution recovery for the evaluation of metastatic bone disease: implementation into routine clinical service. Nuclear Med. Commun. 38, 623–628 (2017). doi:10.1097/MNM.0000000000000686

    Article  Google Scholar 

  12. Ioakemidou, F., Ericson, F., Spuhler, J., Olwal, A., Forsslund, J., Jansson, J., Pysander, E.-L.S., Hoffman, J.: Gestural 3D interaction with a beating heart: simulation, visualization and interaction. In: Proceedings of SIGRAD 2011, KTH, Stockholm, pp. 93–97 (2011)

    Google Scholar 

  13. Ko, Z.Y.G., Mehta, K., Jamil, M., Yap, C.H., Chen, N.: A method to study the hemodynamics of chicken embryo’s aortic arches using optical coherence tomography. J. Biophotonics 10, 353–359 (2017). doi:10.1002/jbio.201600119

    Article  Google Scholar 

  14. Lee, R.C., Darling, C.L., Staninec, M., Ragadio, A., Fried, D.: Activity assessment of root caries lesions with thermal and near-IR imaging methods. J. Biophotonics 10, 433–445 (2017). doi:10.1002/jbio.201500333

    Article  Google Scholar 

  15. Mohammed, I.M., Tatineni, J., Cadd, B., Gibson, I.: Advanced auricular prosthesis development by 3D modelling and multi-material printing. In: Proceedings of the International Conference on Design and Technology. DesTech Conference, Geelong, pp. 37–43 (2017). doi:10.18502/keg.v2i2.593

  16. Murino, L., Granata, D., Carfora, M.F., Selvan, S.E., Alfano, B., Amato, U., La-robina, M.: Evaluation of supervised methods for the classification of major tissues and sub-cortical structures in multispectral brain magnetic resonance images. Comput. Med. Imaging Graph. 38(5), 337–347 (2014). doi:10.1016/j.compmedimag.2014.03.003

    Article  Google Scholar 

  17. Novochadov, V.V., Khoperskov, A.V., Terpilovskiy, A.A., Malanin, D.A., Tiras, K.P., Kovalev, M.E., Astakhov, A.S.: Virtual full-color three-dimensional reconstruction of human knee joint by the digitization of serial layer-by-layer grinding. In: Mathematical Biology and Bioinformatics. Reports of the VI International Conference, Puschino, pp. 76–78 (2016)

    Google Scholar 

  18. Novochadov, V.V., Shiroky, A.A., Khoperskov, A.V., Losev, A.G.: Comparative modeling the thermal transfer in tissues with volume pathological focuses and tissue engineering constructs: a pilot study. Eur. J. Mol. Biotechnol. 14, 125–138 (2016). doi:10.13187/ejmb.2016.14.125

    Google Scholar 

  19. Novochadov, V.V., Terpilovsky, A.A., Shirokiy, A.A., Tiras, K.P., Klimenko, A.S., Klimenko, S.V.: Visual analytics based on recoding input color information in 3D-reconstructions of human bones and joint. In: C-IoT-VRTerro 2016, pp. 257–260. Institute of Physical and Technical Informatics, Protvino (2016)

    Google Scholar 

  20. Papantoniou, I., Sonnaert, M., Geris, L., Luyten, F.P., Schrooten, J., Kerck-hofs, G.: Three-dimensional characterization of tissue-engineered constructs by contrast-enhanced nanofocus computed tomography. Tissue Eng. Part C Methods 20, 177–187 (2014). doi:10.1089/ten.TEC.2013.0041

    Article  Google Scholar 

  21. Polyakov, M.V., Khoperskov, A.V.: Mathematical modeling of radiation fields in biological tissues: the definition of the brightness temperature for the diagnosis. Sci. J. VolSU Math. Phys. 5(36), 73–84 (2016). doi:10.15688/jvolsu1.2016.5.7

    Google Scholar 

  22. Terpilovskij, A.A., Kuz’min, A.L., Lukashkina, R.A.: Method for creating a virtual model of a biological object and a device for its implementation. Patent of the Russian Federation. Invention No. 2418316, 10 May 2011. Bull. 13

    Google Scholar 

  23. Terpilovskiy, A.A., Tiras, K.P., Khoperskov, A.V., Novochadov, V.V.: The possibilities of full-color three-dimensional reconstruction of biological objects by the method of layer-by-layer overlapping: knee joint of a rat. Sci. J. Volgograd State Univ. Nat. Sci. 4, 6–14 (2015). doi:10.15688/jvolsu11.2015.4.1

  24. Turlapov, V.E., Gavrilov, N.I.: 3D scientific visualization and geometric modeling in digital biomedicine. Sci. Vis. 7(4), 27–43 (2015)

    Google Scholar 

  25. Uma Vetri Selvi, G., Nadarajan, R.: A rapid compression technique for 4-D functional MRI images using data rearrangement and modified binary array techniques. Australas. Phys. Eng. Sci. Med. 38, 731–742 (2015). doi:10.1007/s13246-015-0385-y

    Article  Google Scholar 

  26. Weber, L., Langer, M., Tavella, S., Ruggiu, A., Peyrin, F.: Quantitative evaluation of regularized phase retrieval algorithms on bone scaffolds seeded with bone cells. Phys. Med. Biol. 61, 215–231 (2016). doi:10.1088/0031-9155/61/9/N215

    Article  Google Scholar 

  27. Xu, X., Chen, X., Li, F., Zheng, X., Wang, Q., Sun, G., Zhang, J., Xu, B.: Effectiveness of endoscopic surgery for supratentorial hypertensive intracerebral hemorrhage: a comparison with craniotomy. J. Neurosurg. 1–7 (2017). doi:10.3171/2016.10.JNS161589

Download references

Acknowledgments

KAV and AAS are thankful to the Ministry of Education and Science of the Russian Federation (project No. 2.852.2017/4.6). NVV thanks the RFBR grant and Volgograd Region Administration (No. 15-47-02642).

Author information

Authors and Affiliations

  1. Institute of Mathematics and Information Technologies, Volgograd State University, Volgograd, Russia

    A. V. Khoperskov, M. E. Kovalev & A. S. Astakhov

  2. Institute of Computing for Physics and Technology, Protvino, Moscow Oblast, Russia

    A. S. Astakhov

  3. Institute of Natural Sciences, Volgograd State University, Volgograd, Russia

    V. V. Novochadov

  4. The Laboratory of Virtual Biology Ltd., Moscow, Russia

    A. A. Terpilovskiy

  5. Institute of Theoretical and Experimental Biophysics of RAS, Moscow, Russia

    K. P. Tiras

  6. Volgograd State Medical University, Volgograd, Russia

    D. A. Malanin

Authors
  1. A. V. Khoperskov
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. E. Kovalev
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. A. S. Astakhov
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. V. V. Novochadov
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. A. A. Terpilovskiy
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. K. P. Tiras
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. D. A. Malanin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to A. V. Khoperskov , A. S. Astakhov or V. V. Novochadov .

Editor information

Editors and Affiliations

  1. Centre for Applied Informatics, Victoria University, Melbourne, Victoria, Australia

    Siuly Siuly

  2. Vrije University of Amsterdam, Amsterdam, The Netherlands

    Zhisheng Huang

  3. University of Nottingham, Nottingham, United Kingdom

    Uwe Aickelin

  4. Swinburne University of Technology, Melbourne, Victoria, Australia

    Rui Zhou

  5. Victoria University, Melbourne, Victoria, Australia

    Hua Wang

  6. Victoria University, Melbourne, Victoria, Australia

    Yanchun Zhang

  7. Institute for High Energy Physics, Protvino, Russia

    Stanislav Klimenko

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this paper

Cite this paper

Khoperskov, A.V. et al. (2017). Software for Full-Color 3D Reconstruction of the Biological Tissues Internal Structure. In: Siuly, S., et al. Health Information Science. HIS 2017. Lecture Notes in Computer Science(), vol 10594. Springer, Cham. https://doi.org/10.1007/978-3-319-69182-4_1

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-69182-4_1

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-69181-7

  • Online ISBN: 978-3-319-69182-4

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics