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Cross-modal coherent registration of whole mouse brains


Recent whole-brain mapping projects are collecting large-scale three-dimensional images using modalities such as serial two-photon tomography, fluorescence micro-optical sectioning tomography, light-sheet fluorescence microscopy, volumetric imaging with synchronous on-the-fly scan and readout or magnetic resonance imaging. Registration of these multi-dimensional whole-brain images onto a standard atlas is essential for characterizing neuron types and constructing brain wiring diagrams. However, cross-modal image registration is challenging due to intrinsic variations of brain anatomy and artifacts resulting from different sample preparation methods and imaging modalities. We introduce a cross-modal registration method, mBrainAligner, which uses coherent landmark mapping and deep neural networks to align whole mouse brain images to the standard Allen Common Coordinate Framework atlas. We build a brain atlas for the fluorescence micro-optical sectioning tomography modality to facilitate single-cell mapping, and used our method to generate a whole-brain map of three-dimensional single-neuron morphology and neuron cell types.

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Fig. 1: Overview of mBrainAligner.
Fig. 2: Accuracy of mBrainAligner in brain delineation.
Fig. 3: Accuracy of mBrainAligner in computational soma localization and axon projection prediction.
Fig. 4: fMOST-domain atlas of mouse brain.
Fig. 5: Topography of thalamic neuronal projections by integrating Common Coordinate Framework-registered brains.

Data availability

The full resolution fMOST image datasets ( of all mouse brains used in this study, as well as the original and CCFv3 registered single neuron reconstructions (, are available at BICCN’s Brain Image Library (BIL) at Pittsburgh Supercomputing Center ( The single-neuron reconstructions, the CCFv3 registered version of these reconstructions, as well as 3D navigation movie-gallery of these data are also available at SEU-ALLEN Joint Center, Institute for Brain and Intelligence ( The Allen CCFv3 is available at (, and MRI mouse brian used in this study can be obtained through ( We also provided downsampled fMOST, LSFM, VISoR and MRI whole mouse brain data and LSFM partially imaged brain data along with code and testing scripts at Github page ( The full resolution LSFM and VISoR brain images are available on request. Source data are provided with this paper.

Code availability

The source code of all mBrainAligner modules, including stripe artifacts removal, automatic global registration, automatic local registration, semiautomatic refinement along with the binary executable files and sample data can be found at mBrainAligner’s GitHub page ( The automatic global, local registration and semiautomatic registration modules were written in C++ (v.11) with Qt (v.5.6), and the stripe artifacts removal module was implemented using Matlab 2016.


  1. Gong, H. et al. High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level. Nat. Commun. 7, 1–12 (2016).

    Google Scholar 

  2. Economo, M. N. et al. A platform for brain-wide imaging and reconstruction of individual neurons. eLife 5, e10566 (2016).

    PubMed  PubMed Central  Google Scholar 

  3. Osten, P. & Margrie, T. W. Mapping brain circuitry with a light microscope. Nat. Methods 10, 515–523 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Ragan, T. et al. Serial two-photon tomography for automated ex vivo mouse brain imaging. Nat. Methods 9, 255–258 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Wang, H. et al. Scalable volumetric imaging for ultrahigh-speed brain mapping at synaptic resolution. Natl Sci. Rev. 6, 982–992 (2019).

    PubMed  PubMed Central  Google Scholar 

  6. Xu, F. et al. High-throughput mapping of a whole rhesus monkey brain at micrometer resolution. Nat. Biotechnol. (2021).

  7. Niedworok, C. J. et al. Charting monosynaptic connectivity maps by two-color light-sheet fluorescence microscopy. Cell Rep. 2, 1375–1386 (2012).

    CAS  PubMed  Google Scholar 

  8. Dodt, H.-U. et al. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat. Methods 4, 331–336 (2007).

    CAS  PubMed  Google Scholar 

  9. Chung, K., Wallace, J., Kim, S. Y., Kalyanasundaram, S. & Deisseroth, K. Structural and molecular interrogation of intact biological systems. Nature 497, 332–337 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Tomer, R., Ye, L., Hsueh, B. & Deisseroth, K. Advanced CLARITY for rapid and high-resolution imaging of intact tissues. Nat. Protoc. 9, 1682–1697 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Murray, E. et al. Simple, scalable proteomic imaging for high-dimensional profiling of intact systems. Cell 163, 1500–1514 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Renier, N. et al. iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging. Cell 159, 896–910 (2014).

    CAS  PubMed  Google Scholar 

  13. Pan, C. et al. Shrinkage-mediated imaging of entire organs and organisms using uDISCO. Nat. Methods 13, 859–867 (2016).

    CAS  PubMed  Google Scholar 

  14. Susaki, E. A. et al. Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging. Nat. Protoc. 10, 1709–1727 (2015).

    CAS  PubMed  Google Scholar 

  15. Richardson, D. S. & Lichtman, J. W. Clarifying tissue clearing. Cell 162, 246–257 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Thomas, R., Smallwood, P. M., John, W., Jeremy, N. & Eshel, B. J. Genetically-directed, cell type-specific sparse labeling for the analysis of neuronal morphology. PLoS One 3, e4099 (2008).

    Google Scholar 

  17. Aransay, A., Rodríguez-López, C., García-Amado, M., Clascá, F. & Prensa, L. Long-range projection neurons of the mouse ventral tegmental area: a single-cell axon tracing analysis. Front. Neuroanat. 9, 59 (2015).

    PubMed  PubMed Central  Google Scholar 

  18. Ghosh, S. et al. Sensory maps in the olfactory cortex defined by long-range viral tracing of single neurons. Nature 472, 217–220 (2011).

    CAS  PubMed  Google Scholar 

  19. Lin, R. et al. Cell-type-specific and projection-specific brain-wide reconstruction of single neurons. Nat. Methods 15, 1033–1036 (2018).

    CAS  PubMed  Google Scholar 

  20. Wang, Y. et al. TeraVR empowers precise reconstruction of complete 3-D neuronal morphology in the whole brain. Nat. Commun. 10, 3474 (2019).

    PubMed  PubMed Central  Google Scholar 

  21. Winnubst, J. et al. Reconstruction of 1,000 projection neurons reveals new cell types and organization of long-range connectivity in the mouse brain. Cell 179, 268–281.e213 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Zhou, H. et al. GTree: an Open-source tool for dense reconstruction of brain-wide neuronal population. Neuroinformatics 19, 305–317 (2020).

    Google Scholar 

  23. Peng, H. et al. BigNeuron: large-scale 3D neuron reconstruction from optical microscopy images. Neuron 87, 252–256 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Ecker, J. R. et al. The BRAIN initiative cell census consortium: Lessons learned toward generating a comprehensive brain cell atlas. Neuron 96, 542–557 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Oh, S. W. et al. A mesoscale connectome of the mouse brain. Nature 508, 207–214 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Zingg, B., Hintiryan, H., Gou, L., Song, M. Y. & Dong, H.-W. Neural Networks of the Mouse Neocortex. Cell 156, 1096–1111 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Hintiryan, H. et al. The mouse cortico-striatal projectome. Nat. Neurosci. 19, 1100–1114 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Bienkowski, M. S. et al. Integration of gene expression and brain-wide connectivity reveals the multiscale organization of mouse hippocampal networks. Nat. Neurosci. 21, 1628–1643 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Dong, H. W. The Allen Reference Atlas: A Digital Color Brain Atlas of the C57Bl/6J Male Mouse (John Wiley & Sons Inc., 2008).

  30. Wang, Q. et al. The Allen mouse brain common coordinate framework: a 3D reference atlas. Cell 181, 936–953.e920 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Perens, J. et al. An optimized mouse brain atlas for automated mapping and quantification of neuronal activity using iDISCO+ and light sheet fluorescence microscopy. Neuroinformatics 19, 433–446 (2020).

    PubMed Central  Google Scholar 

  32. Peng, H. et al. Morphological diversity of single neurons in molecularly defined cell types. Nature 598, 174–181 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Long, F., Peng, H., Liu, X., Kim, S. K. & Myers, E. A 3D digital atlas of C. elegans and its application to single-cell analyses. Nat. Methods 6, 667–672 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Peng, H. et al. BrainAligner: 3D registration atlases of Drosophila brains. Nat. Methods 8, 493–500 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Randlett, O. et al. Whole-brain activity mapping onto a zebrafish brain atlas. Nat. Methods 12, 1039–1046 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Griffiths, V. A. et al. Real-time 3D movement correction for two-photon imaging in behaving animals. Nat. Methods 17, 741–748 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Avants, B. B., Tustison, N. & Song, G. Advanced normalization tools (ANTS). Insight J. 2, 1–35 (2009).

    Google Scholar 

  38. Klein, S., Staring, M., Murphy, K., Viergever, M. A. & Pluim, J. P. W. Elastix: a toolbox for intensity-based medical image registration. IEEE Trans. Med. Imaging 29, 196–205 (2009).

    PubMed  Google Scholar 

  39. Modat, M. et al. Fast free-form deformation using graphics processing units. Computer Methods Prog. Biomedicine 98, 278–284 (2010).

    Google Scholar 

  40. Niedworok, C. J. et al. aMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data. Nat. Commun. 7, 1–9 (2016).

    Google Scholar 

  41. Renier, N. et al. Mapping of brain activity by automated volume analysis of immediate early genes. Cell 165, 1789–1802 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Goubran, M. et al. Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI. Nat. Commun. 10, 1–17 (2019).

    Google Scholar 

  43. Fan, J., Cao, X., Yap, P.-T. & Shen, D. BIRNet: brain image registration using dual-supervised fully convolutional networks. Med. Image Anal. 54, 193–206 (2019).

    PubMed  PubMed Central  Google Scholar 

  44. Cao, X., Yang, J., Zhang, J., Nie, D., Kim, M., Wang, Q., & Shen, D. Deformable image registration based on similarity-steered CNN regression. In Proc. International Conference on Medical Image Computing and Computer-Assisted Intervention (eds. Descoteaux M., Maier-Hein L., Franz A., Jannin P., Collins D., Duchesne S.) 300–308 (Springer, Cham, 2017).

  45. Zeng, H. & Sanes, J. R. Neuronal cell-type classification: challenges, opportunities and the path forward. Nat. Rev. Neurosci. 18, 530–546 (2017).

    CAS  PubMed  Google Scholar 

  46. Harris, J. A. et al. Hierarchical organization of cortical and thalamic connectivity. Nature 575, 195–202 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Muñoz-Castaneda, R. et al. Cellular anatomy of the mouse primary motor cortex. Nature 598, 159–166 (2021).

    PubMed  PubMed Central  Google Scholar 

  48. Jones, E. G. The Thalamus (Springer Science & Business Media, 2012).

  49. Tward, D. J. et al. Solving the where problem in neuroanatomy: a generative framework with learned mappings to register multimodal, incomplete data into a reference brain. Preprint at bioRxiv (2020).

  50. Ramon y Cajal, S. Histologie du système nerveux de l’homme et des vertébrés. Maloine, Paris 2, 153–173 (1911).

    Google Scholar 

  51. 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, 348–353 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Chi, J. et al. Three-dimensional adipose tissue imaging reveals regional variation in beige fat biogenesis and PRDM16-dependent sympathetic neurite density. Cell Metab. 27, 226–236.e223 (2018).

    CAS  PubMed  Google Scholar 

  53. Otsu, N. A threshold selection method from gray-level histograms. IEEE Trans. Syst. Man Cybern. 9, 62–66 (2007).

    Google Scholar 

  54. HL, C. & Rangarajan, A. A new point matching algorithm for non-rigid registration. Computer Vis. Image Underst. 89, 114–141 (2003).

    Google Scholar 

  55. Harris, C. G. & Stephens, M. A combined corner and edge detector. in Proc. Alvey Vision Conference Vol. 15, 10–5244 (Citeseer, 1988).

  56. Wahba, G. Spline Models for Observational Data (SIAM, 1990).

  57. Qu, L. & Peng, H. Littlequickwarp: an ultrafast image warping tool. Methods 73, 38–42 (2015).

    CAS  PubMed  Google Scholar 

  58. Dalal, N. & Triggs, B. Histograms of oriented gradients for human detection. In Proc. Computer Society Conference on Computer Vision and Pattern Recognition Vol. 1 886–893 (IEEE, 2005).

  59. Çiçek, Ö., Abdulkadir, A., Lienkamp, S. S., Brox, T. & Ronneberger, O. 3D U-Net: learning dense volumetric segmentation from sparse annotation. In Proc. International Conference on Medical Image Computing and Computer-assisted Intervention (eds. Ourselin S., Joskowicz L., Sabuncu M., Unal G., Wells W) 424–432 (Springer, 2016).

  60. Fürth, D. et al. An interactive framework for whole-brain maps at cellular resolution. Nat. Neurosci. 21, 139–149 (2018).

    PubMed  Google Scholar 

  61. Mortensen, E. N. & Barrett, W. A. Intelligent scissors for image composition. In Proc. 22nd Annual Conference on Computer Graphics and Interactive Techniques 191–198 (ACM TOG, 1995).

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This work was initialized and funded by Southeast University to support Open Science collaboration through the SEU-ALLEN Joint Center, Institute of Brain and Intelligence. We thank Y. Wang and Q. Wang (Allen Institute for Brain Science) for assistance with manual annotation of some somas, Y. Yu (Allen Institute for Brain Science) for downsampling several fMOST datasets, S. Jiang (Southeast University) for assistance in data storage and transmission, D.H. Lu (Tencent) for building mBrainAligner’s web portal interface, M. Dierssen (Center for Genomic Regulation) and L. Manubens-Gil (Southeast University) for providing partial brain LSFM data, W. Luo, H. Wang, J. Yang, M. Wang, Y. Tang and R. Zhang (Anhui University) for help with semiautomatic registration, the team at SEU-ALLEN Joint Center for neuron reconstruction, and the supercomputing platform of Anhui University for computing support. This work was also partially funded by the National Science Foundation of China (NSFC) grant 61871411 and the University Synergy Innovation Program of Anhui Province GXXT-2019-008 and GXXT-2021-001 to L.Q., the NSFC grant 32071367 to Y.W., the NSFC-Guangdong Joint Fund U20A6005 to G.B. and the Fundamental Research Funds for the Central Universities 2242021k30046.

Author information

Authors and Affiliations



H.P. conceptualized the study and provided guidance for this study. L.Q. led the development of mBrainAligner. H.P., L.Q., P.X., Li L. and Y.L. designed all experiments. L.Q. and Y.L. designed and implemented the CLM. Y.L. conducted validation analyses of mBrainAligner, generated the fMOST atlas and created the figures. Y.L. designed and Long L. developed the semiautomatic registration module. Long L. designed and implemented the 2.5D corner detection algorithm. L.Q. and W.W. designed and implemented the stripe artifacts removal tool. L.Q. and T.W. codeveloped tools for image and various neuronal structure warping, and T.W. assisted in building the fMOST atlas. K.G. and Y.Z. collaborated on deep-learning models. L.O. developed the global registration module. F.X. developed registration scripts and helped in aligning neurons to CCF. J.W. and Y.L. collaborated with L.Q. to set up and manage the software-developing team and the data-analyzing team. P.X. conducted the cell type analysis and provided tools for soma localization and axon projection analyses. Li L. provided and validated soma localization and axon projection data. Y.W. contributed to neuronal reconstruction. H.G. and Q.L. provided the fMOST imaging data. A.K. and Z.W. provided the LSFM imaging data. F.X. and G.B. provided the VISoR imaging data. H.D. assisted in anatomy analysis. H.Z. provided the fMOST dataset. H.P., L.Q. and Y.L. wrote the manuscript with input from all coauthors.

Corresponding author

Correspondence to Hanchuan Peng.

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Competing interests

The authors declare no competing interests.

Additional information

Peer review Information Nature Methods thanks the anonymous reviewers for their contribution to the peer review of this work. Nina Vogt was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Semi-automatic registration.

a, Interface of semi-automatic registration module. b, Three levels of sub-region granularity (coarse, medium, and fine) are provided for each main brain region. c-h, Comparison of registration accuracy on 31 fMOST brains when semi-automatic registration is applied after automatic registration. Box plot: center line, median; box limits, upper and lower quartiles; whiskers, 1.5 x interquartile range; points, outliers.

Source data

Extended Data Fig. 2 Architecture and performance of deep learning-based segmentation network.

a, Architecture of segmentation network. b, 3D visualization of segmentation results of six brain regions. c-d, Comparison of registration accuracy of mBrainAligner on 31 fMOST brains with deep learning features toggled on and off. Box plot: center line, median; box limits, upper and lower quartiles; whiskers, 1.5 x interquartile range; points, outliers.

Source data

Extended Data Fig. 3 Comparison of different methods in registering images of different modalities to CCFv3.

Four green dashed boxes show the brain registration results of four different modalities (LSFM, VISoR, MRI, fMOST) generated by different methods (MIRACL, ClearMap, aMAP and mBrainAligner,). The first and second rows of each box show the coronal and sagittal view of registered brains respectively with zoom-in view of two subregions. Registered brains of different modalities with brain region boundaries (orange) defined in CCFv3 overlaid. In each box, arrows of the same color point to the same spatial coordinates.

Extended Data Fig. 4 Comparison of soma localization between manual annotation and computational prediction results generated by different methods.

The left side of diagram shows manually annotated results, and the right side shows their computationally predicted results.

Extended Data Fig. 5 Comparison of neuron mapping results generated by different methods.

a-f, 63 CCFv3 mapped neurons of six brains (ID 17302, 17545, 18454, 18455, 18457 and 18464) with somas residing in VPM or VPL. The first row of a-f shows CCFv3 aligned brains generated by four different methods (mBrainAligner, MIRACL, ClearMap and aMAP). The cross-lines overlaid on the aligned brains point to the same coordinate on the inner boundary of cortex. The left-most image of second row of a-f shows corresponding slice of CCFv3 average template, and the right three images show the maximum intensity projection view of CCFv3 with mapped neurons overlaid, with red for mBrainAligner, green for MIRACL, yellow for ClearMap and purple for aMAP.

Extended Data Fig. 6 fMOST-domain atlas of mouse brain (2D views).

Coronal sections of fMOST-domain atlas of mouse brain, with average template shown on left and annotation template on right.

Extended Data Fig. 7 Topography of thalamic neuron projections by integrating CCF-registered brains.

a, Location of axonal arbors of cortical projection neurons grouped by thalamic nuclei. Dots represent center of axonal arbors in the flattened 2D cortical map. Locations of corresponding somas are color-coded in three separate columns: (left to right) the anterior-posterior (soma-x), dorsal-ventral (soma-y) and lateral-medial (soma-z) axes. b, Examples of single-neuron projections (VPL, LGd, MG). Colors represent individual neurons.

Extended Data Fig. 8 Stripe artifacts removal.

a, One coronal slice of fMOST mouse brain image. b, The Fourier spectrum of image shown in a. c, Constructed Gaussian notch filter. d, Log transformed image of a. e, Filtered spectrum of log-transformed image using filter as shown in c. f, Image after stripe removal.

Extended Data Fig. 9 Partial image alignment.

a, Partially imaged brain region of hippocampus (in LSFM modality). b, Global alignment result of partial image to CCFv3. The left column shows the maximum intensity projection of globally aligned partial brain (top) and its blended view with CCFv3 average template (bottom), with their three-view shown on the right. c, Result after semi-automatic refinement.

Supplementary information

Reporting Summary

Supplementary Video 1

Stripe artifacts removal.

Supplementary Video 2

Global registration of mouse brain.

Supplementary Video 3

Coherent landmark mapping.

Supplementary Video 4

Semiautomatic registration of mouse brain.

Source data

Source Data Fig. 2

Statistical source data of Fig.2b.

Source Data Fig. 3

Statistical source data of Fig.3c,i.

Source Data Fig. 4

Statistical source data of Fig.4d.

Source Data Extended Data Fig. 1

Statistical source data of Extended Data Fig.1c,d.

Source Data Extended Data Fig. 2

Statistical source data of Extended Data Fig.2c,d.

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Qu, L., Li, Y., Xie, P. et al. Cross-modal coherent registration of whole mouse brains. Nat Methods 19, 111–118 (2022).

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