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Advances in Bio-Imaging: From Physics to Signal Understanding Issues pp 173–190Cite as

Computational Approaches for the Processing of Cerebral Histological Images of Small Animals

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Part of the book series: Advances in Intelligent and Soft Computing ((AINSC,volume 120))

Abstract

Histological sections of tissue have been studied for many decades and constitute one the most prevalent means of information on biological processes and functions for animals. With the introduction of digital images in medicine, image processing techniques derived from medical imaging were adapted to scanned histological sections in order to improve their visualization and analysis. More recently, the introduction of virtual microscopy yet increased the interest of analyzing histological sections on a computer screen and opened up a whole branch of biomedical image processing dedicated to the extraction of information contained in histological sections at very high magnification. In this work we present three novel approaches to study histological sections of the brain in small animals: 1) the alignment of histological sections to create a 3D image, 2) the processing of very large microscopy sections and 3) the correlation of histological sections with 3D in vivo images acquired on medical imaging devices.

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References

  1. Akselrod-Ballin, A., Bock, D., Reid, R.C., Warfield, S.K.: In: Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2009), Improved registration for large electron microscopy images, Boston, MA, USA, pp. 434–437 (2009)

    Google Scholar 

  2. Andreasen, A., Drewes, A.M., Assentoft, J.E., Larsen, N.E.: Computer-assisted alignment of standard serial sections without use of artificial landmarks. A practical approach to the utilization of incomplete information in 3-D reconstruction of the hippocampal region. Journal of Neuroscience Methods, 45(3),199–207 (1992)

    Google Scholar 

  3. Arsigny, V., Pennec, X., Ayache, N.: Medical Image Analysis, Polyrigid and Polyaffine Transformations: a Novel Geometrical Tool to Deal with Non-Rigid Deformations - Application to the registration of histological slices 6(9), 507–523 (2005)

    Google Scholar 

  4. Bardinet, E., Bhattacharjee, M., Dormont, D., Pidoux, B., Malandain, G., Schupbach, S., Ayache, N., Ornu, P., Agid, Y., Yelnik, J.: A three-dimensional histological atlas of the human basal ganglia. II. Atlas deformation strategy and evaluation in deep brain stimulation for Parkinson disease. Journal of Neurosurgery 2, 208–219 (2009)

    Article  Google Scholar 

  5. Ceritoglu, C., Wang, L., Selemon, L.D., Csernansky, J.G., Miller, M.I., Ratnanather, J.T.: Large deformation diffeomorphic metric mapping registration of reconstructed 3D histological section images and in vivo MR images. Frontiers in Human Neuroscience 5, 12 (2010)

    Google Scholar 

  6. Chakravarty, M.M., Bertrand, G., Hodge, C.P., Sadikot, A.F., Collins, D.L.: The creation of a brain atlas for image guided neurosurgery using serial histological data. NeuroImage 30(2), 359–376 (2006)

    Article  Google Scholar 

  7. Christensen, G., Joshi, S., Miller, M.: Volumetric transformation of brain anatomy. IEEE Trans. Med. Imaging 16, 864–877 (1997)

    Article  Google Scholar 

  8. Dauguet, J.: École Centrale de Paris. L’imagerie post mortem tridimensionnelle cérébrale: constitution et apport pour l’analyse conjointe de données histologiques anatomo-fonctionnelles et la mise en correspondance avec l’imagerie in vivo (2005)

    Google Scholar 

  9. Dauguet, J., Delzescaux, T., Condé, F., Mangin, J.-F., Ayache, N., Hantraye, P., Frouin, V.: Three-dimensional reconstruction of stained histological slices and 3D non-linear registration with in-vivo MRI for whole baboon brain. Journal of Neuroscience Methods 164(1), 191–204 (2007)

    Article  Google Scholar 

  10. Dauguet, J., Peled, S., Berezovskii, V., Delzescaux, T., Warfield, S.K., Born, R., Westin, C.-F.: Comparison of fiber tracts derived from In-Vivo DTI tractography with 3D histological neural tract tracer reconstruction on a macaque brain. NeuroImage 37(2), 530–538 (2007)

    Article  Google Scholar 

  11. Dauguet, J., Dock, D., Reid, R.C., Warfield, S.K.: Alignment of large image series using cubic B-splines tessellation: Application to transmission electron microscopy data. In: Ayache, N., Ourselin, S., Maeder, A. (eds.) MICCAI 2007, Part II. LNCS, vol. 4792, pp. 710–717. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  12. Dauguet, J., Condé, F., Hantraye, P., Frouin, V., Delzescaux, T.: Generation of a 3D atlas of the nuclear division of the thalamus based on histological sections of primate: intra- and inter-subject atlas-to-MRI warping. In: IRBM, vol. 30(5-6), pp. 281–291 (2009)

    Google Scholar 

  13. Dauguet, J., Hérard, A.-S., Declerck, J., Delzescaux, T.: Locally constrained cubic B-spline deformations to control volume variations. In: Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2009), Boston, MA, USA (2009)

    Google Scholar 

  14. Dauguet, J., de Primatologie, R.: Three-dimensional histological imaging of primate brain and correlation with in vivo medical device images 4, 2 (2010), http://primatologie.revues.org/

    Google Scholar 

  15. Dhenain, M., El Tannir El Tayara, N., Wu, T.D., Guégan, M., Volk, A., Quintana, C., Delatour, B.: Characterization of in vivo MRI detectable thalamic amyloid plaques from APP/PS1 mice. Neurobiol. Aging 1, 41–53 (2009)

    Article  Google Scholar 

  16. Dubois, A., Dauguet, J., Hérard, A.-S., Besret, L., Duchesnay, E., Frouin, V., Hantraye, P., Bonvento, G., Delzescaux, T.: Automated three-dimensional analysis of histological and autoradiographic rat brain sections: application to an activation study. J. Cereb. Blood Flow Metab. 10(27), 1742–1755 (2007)

    Article  Google Scholar 

  17. Dubois, A., Hérard, A.-S., Delatour, B., Hantraye, P., Bonvento, G., Dhenain, M., Delzescaux, T.: Detection by voxel-wise statistical analysis of significant changes in regional cerebral glucose uptake in an APP/PS1 transgenic mouse model of Alzheimer’s disease. NeuroImage 51(2), 586–598 (2010)

    Article  Google Scholar 

  18. Golgi, C.: On the structure of the brain grey matter. Gazzetta Medica Italiana lombarda 6, 244–246 (1873)

    Google Scholar 

  19. Hibbard, L.S., Hawkins, R.A.: Objective image alignment for three-dimensional reconstruction of digital autoradiograms. J. Neurosci. Methods 26(1), 55–74 (1988)

    Article  Google Scholar 

  20. Ikonomovic, M.D., Klunk, W.E., Abrahamson, E.E., Mathis, C.A., Price, J.C., Tsopelas, N.D., Lopresti, B.J., Ziolko, S., Bi, W., Paljug, W.R., Debnath, M.L., Hope, C.E., Isanski, B.A., Hamilton, R.L., DeKosky, S.T.: Post-mortem correlates of in vivo PiB-PET amyloid imaging in a typical case of Alzheimer’s disease. Brain 131(6), 1630–1645 (2008)

    Article  Google Scholar 

  21. Johnson, G.A., Cofer, G.P., Fubara, B., Gewalt, S.L., Hedlund, L.W., Maronpot, R.R.: Magnetic resonance histology for morphologic phenotyping. J. Magn. Reson. Imaging 16(4), 423–429 (2002)

    Article  Google Scholar 

  22. Kim, B., Boes, J.L., Frey, K.A., Meyer, C.R.: Mutual information for automated unwarping of rat brain autoradiographs. Neuroimage 5(1), 31–40 (1997)

    Article  Google Scholar 

  23. Laan, A., Lamers, W., Huijsmans, D., Kortschot, A.T., Smith, J., Strackee, J., Los, J.: Deformation-corrected computer-aided three-dimensional reconstruction of immunohistochemically stained organs: application to the rat heart during early organogenesis. The Anatomical Record 224, 443–457 (1989)

    Article  Google Scholar 

  24. Lebenberg, J., Herard, A.-S., Dubois, A., Dauguet, J., Frouin, V., Dhenain, M., Hantraye, P., Delzescaux, T.: Validation of MRI-based 3D digital atlas registration with histological and autoradiographic volumes: an anatomofunctional transgenic mouse brain imaging study. Neuroimage 51(3), 1037–1046 (2010)

    Article  Google Scholar 

  25. Lin, G., Bjornsson, C.S., Smith, K.L., Abdul-Karim, M.-A., Turner, J.N., Shain, W., Roysam, B.: Automated image analysis methods for 3-D quantification of the neurovascular unit from multichannel confocal microscope images. Cytometry 66A, 9–23 (2005)

    Article  Google Scholar 

  26. Malandain, G., Bardinet, E., Nelissen, K., Vanduffel, W.: Fusion of autoradiographs with an MR volume using 2-D and 3-D linear transformations. NeuroImage 23(1), 111–127 (2004)

    Article  Google Scholar 

  27. Mega, M.S., Chen, S.S., Thompson, P.M., Woods, R.P., Karaca, T.J., Tiwari, A., Vinters, H.V., Small, G.W., Toga, A.W.: Mapping histology to metabolism: coregistration of stained whole-brain sections to premortem PET in Alzheimer’s disease. Neuroimage 5(2), 147–153 (1997)

    Article  Google Scholar 

  28. Mikula, S., Trotts, I., Stone, J.M., Jones, E.G.: Internet-enabled high-resolution brain mapping and virtual microscopy. Neuroimage 35(1), 9–15 (2007)

    Article  Google Scholar 

  29. Indhumathi, C., Cai, Y., Guan, Y., Opas, M.: An automatic segmentation algorithm for 3D cell cluster splitting using volumetric confocal images. Journal of Microscopy (in Press)

    Google Scholar 

  30. Ourselin, S., Roche, A., Subsol, G., Pennec, X., Ayache, N.: Reconstructing a 3D Structure from Serial Histological Sections. Image and Vision Computing 19(1-2), 25–31 (2001)

    Article  Google Scholar 

  31. Peng, H., Ruan, Z., Long, F., Simpson, J.H., Myers, E.W.: V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nat. Biotechnol. 28(4), 348–353 (2010)

    Article  Google Scholar 

  32. Pitiot, A., Bardinet, E., Thompson, P.M., Malandain, G.: Piecewise Affine Registration of Biological Images for Volume Reconstruction. Medical Image Analysis 10(3), 465–483 (2006)

    Article  Google Scholar 

  33. Ramon y Cajal, S.: Manual de Histologia normal y Tecnica micrografica (1889)

    Google Scholar 

  34. Rydmark, M., Jansson, T., Berthold, C.H., Gustavsson, T.: Computer-assisted realignment of light micrograph images from consecutive section series of cat cerebral cortex. J. Microsc. 165(1), 29–47 (1992)

    Article  Google Scholar 

  35. Schormann, T., Dabringhaus, A., Zilles, K.: Statistics of deformations in histology and application to improved alignment with MRI. IEEE Trans. Med. Imaging 14(1), 25–35 (1995)

    Article  Google Scholar 

  36. Schormann, T., Zilles, K.: Three-Dimensional Linear and Nonlinear Transformations: An Integration of Light Microscopical and MRI Data. Human Brain Mapping 6, 339–347 (1998)

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. CEA-CNRS, MIRCen, Route du Panorama, 92265, Fontenay-aux-Roses, France

    Julien Dauguet

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  1. Julien Dauguet
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Correspondence to Julien Dauguet .

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Editors and Affiliations

  1. IPAL, I2R & CNRS, 1 Fusionoplis Way #10-18, Singapore, 138632, Singapore

    Nicolas Loménie

  2. IPAL, I2R & CNRS, 1 Fusionoplis Way #21-01, Singapore, 138632, Singapore

    Daniel Racoceanu

  3. Singapore Immunology Network (SIgN), 8A Biomedical Grove, Immunos Building, Level 4, Singapore, 138648, Singapore

    Alexandre Gouaillard

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© 2012 Springer Berlin Heidelberg

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Dauguet, J. (2012). Computational Approaches for the Processing of Cerebral Histological Images of Small Animals. In: Loménie, N., Racoceanu, D., Gouaillard, A. (eds) Advances in Bio-Imaging: From Physics to Signal Understanding Issues. Advances in Intelligent and Soft Computing, vol 120. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-25547-2_11

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  • DOI: https://doi.org/10.1007/978-3-642-25547-2_11

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