Abdelmoula, W. M., Carreira, R. J., Shyti, R., Balluff, B., van Zeijl, R. J., Tolner, E. A., Lelieveldt, B. F., van den Maagdenberg, A. M., McDonnell, L. A., & Dijkstra, J. (2014). Automatic registration of mass spectrometry imaging data sets to the Allen brain Atlas. Analytical Chemistry, 86(8), 3947–3954.
Article CAS PubMed Google Scholar
Agarwal, N., Xu, X., & Gopi, M. (2017). Automatic detection of histological artifacts in mouse brain slice images. In Medical Computer Vision and Bayesian and Graphical Models for Biomedical Imaging: MICCAI 2016 International Workshops, MCV and BAMBI, Athens, Greece, October 21, 2016, Revised Selected Papers 8 (pp. 105–115). Springer.
Allen Institute. Allen Mouse Brain Atlas. Retrieved March 2020, from: http://mouse.brain-map.org/
Allen Institute. Informatics Archive of the Allen Institute. Retrieved January 2021, from: http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/
Bai, J., Trinh, T. L. H., Chuang, K.-H., & Qiu, A. (2012). Atlas-based automatic mouse brain image segmentation revisited: Model complexity vs. image registration. Magnetic Resonance Imaging, 30(6), 789–798.
Beg, M. F., Miller, M. I., Trouvé, A., & Younes, L. (2005). Computing large deformation metric mappings via geodesic flows of diffeomorphisms. International Journal of Computer Vision, 61, 139–157.
Carey, H., Pegios, M., Martin, L., Saleeba, C., Turner, A., Everett, N., Puchades, M., Bjaalie, J., & McMullan, S. (2022). Deepslice: Rapid fully automatic registration of mouse brain imaging to a volumetric atlas. bioRxiv, 2022–04.
Dice, L. R. (1945). Measures of the amount of ecologic association between species. Ecology, 26(3), 297–302.
He, K., Zhang, X., Ren, S., & Sun, J. (2016). Deep residual learning for image recognition. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (pp. 770–778).
Iqbal, A., Sheikh, A., & Karayannis, T. (2019). Denerd: High-throughput detection of neurons for brain-wide analysis with deep learning. Scientific Reports, 9(1), 13828.
Article PubMed PubMed Central Google Scholar
ITK. Insight Segmentation and Registration Toolkit. Retrieved April 2020, from: https://itk.org
Jin, M., Nguyen, J. D., Weber, S. J., Mejias-Aponte, C. A., Madangopal, R., & Golden, S. A. (2022). Smart: An open-source extension of wholebrain for intact mouse brain registration and segmentation. Eneuro, 9(3).
Kim, Y., Venkataraju, K. U., Pradhan, K., Mende, C., Taranda, J., Turaga, S. C., Arganda-Carreras, I., Ng, L., Hawrylycz, M. J., Rockland, K. S., et al. (2015). Mapping social behavior-induced brain activation at cellular resolution in the mouse. Cell reports, 10(2), 292–305.
Article CAS PubMed Google Scholar
Krepl, J., Casalegno, F., Delattre, E., Erö, C., Lu, H., Keller, D., Rodarie, D., Markram, H., & Schürmann, F. (2021). Supervised learning with perceptual similarity for multimodal gene expression registration of a mouse brain atlas. Frontiers in Neuroinformatics, 15, 691918.
Article PubMed PubMed Central Google Scholar
Lein, E. S., Hawrylycz, M. J., Ao, N., Ayres, M., Bensinger, A., Bernard, A., Boe, A. F., Boguski, M. S., Brockway, K. S., Byrnes, E. J., et al. (2007). Genome-wide atlas of gene expression in the adult mouse brain. Nature, 445(7124), 168–176.
Article CAS PubMed Google Scholar
Leung, K. K., Barnes, J., Ridgway, G. R., Bartlett, J. W., Clarkson, M. J., Macdonald, K., Schuff, N., Fox, N. C., Ourselin, S., Initiative, A. D. N., et al. (2010). Automated cross-sectional and longitudinal hippocampal volume measurement in mild cognitive impairment and Alzheimer’s disease. Neuroimage, 51(4), 1345–1359.
Lin, R., Wang, R., Yuan, J., Feng, Q., Zhou, Y., Zeng, S., Ren, M., Jiang, S., Ni, H., Zhou, C., et al. (2018). Cell-type-specific and projection-specific brain-wide reconstruction of single neurons. Nature Methods, 15(12), 1033–1036.
Article CAS PubMed Google Scholar
Maes, F., Collignon, A., Vandermeulen, D., Marchal, G., & Suetens, P. (1997). Multimodality image registration by maximization of mutual information. IEEE transactions on Medical Imaging, 16(2), 187–198.
Article CAS PubMed Google Scholar
Maintz, J. A., & Viergever, M. A. (1998). A survey of medical image registration. Medical Image Analysis, 2(1), 1–36.
Article CAS PubMed Google Scholar
Majka, P., & Wójcik, D. K. (2016). Possum-a framework for three-dimensional reconstruction of brain images from serial sections. Neuroinformatics, 14, 265–278.
Miyamichi, K., Amat, F., Moussavi, F., Wang, C., Wickersham, I., Wall, N. R., Taniguchi, H., Tasic, B., Huang, Z. J., He, Z., et al. (2011). Cortical representations of olfactory input by trans-synaptic tracing. Nature, 472(7342), 191–196.
Article CAS PubMed Google Scholar
Neurodata. (2023). Ardent python package. Retrieved June 2020, from: https://ardent.neurodata.io
Niedworok, C. J., Brown, A. P., Jorge Cardoso, M., Osten, P., Ourselin, S., Modat, M., & Margrie, T. W. (2016). amap is a validated pipeline for registration and segmentation of high-resolution mouse brain data. Nature Communications, 7(1), 11879.
Article PubMed PubMed Central Google Scholar
Ni, H., Tan, C., Feng, Z., Chen, S., Zhang, Z., Li, W., Guan, Y., Gong, H., Luo, Q., & Li, A. (2020). A robust image registration interface for large volume brain atlas. Scientific Reports, 10(1), 1–16.
Oh, S. W., Harris, J. A., Ng, L., Winslow, B., Cain, N., Mihalas, S., Wang, Q., Lau, C., Kuan, L., Henry, A. M., et al. (2014). A mesoscale connectome of the mouse brain. Nature, 508(7495), 207–214.
Article CAS PubMed PubMed Central Google Scholar
Pallast, N., Wieters, F., Fink, G. R., & Aswendt, M. (2019). Atlas-based imaging data analysis tool for quantitative mouse brain histology (Aidahisto). Journal of Neuroscience Methods, 326, 108394.
Article CAS PubMed Google Scholar
Papp, E. A., Leergaard, T. B., Calabrese, E., Johnson, G. A., & Bjaalie, J. G. (2014). Waxholm space atlas of the sprague dawley rat brain. Neuroimage, 97, 374–386.
Paşca, S. P. (2018). The rise of three-dimensional human brain cultures. Nature, 553(7689), 437–445.
Piluso, S., Souedet, N., Jan, C., Clouchoux, C., & Delzescaux, T. (2021). Automated atlas-based segmentation of single coronal mouse brain slices using linear 2D-2d registration. In 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC) (pp. 2860–2863). IEEE.
Puchades, M. A., Csucs, G., Ledergerber, D., Leergaard, T. B., & Bjaalie, J. G. (2019). Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the Quicknii tool. PloS one, 14(5), 0216796.
Qu, L., Li, Y., Xie, P., Liu, L., Wang, Y., Wu, J., Liu, Y., Wang, T., Li, L., Guo, K., et al. (2022). Cross-modal coherent registration of whole mouse brains. Nature Methods, 19(1), 111–118.
Article CAS PubMed Google Scholar
Ragan, T., Kadiri, L. R., Venkataraju, K. U., Bahlmann, K., Sutin, J., Taranda, J., Arganda-Carreras, I., Kim, Y., Seung, H. S., & Osten, P. (2012). Serial two-photon tomography for automated ex vivo mouse brain imaging. Nature Methods, 9(3), 255–258.
Article CAS PubMed PubMed Central Google Scholar
Ramos-Prats, A., Paradiso, E., Castaldi, F., Sadeghi, M., Mir, M. Y., Hörtnagl, H., Göbel, G., & Ferraguti, F. (2022). VIP-expressing interneurons in the anterior insular cortex contribute to sensory processing to regulate adaptive behavior. Cell Reports, 39(9), 110893.
Article CAS PubMed Google Scholar
Renier, N., Adams, E. L., Kirst, C., Wu, Z., Azevedo, R., Kohl, J., Autry, A. E., Kadiri, L., Venkataraju, K. U., Zhou, Y., et al. (2016). Mapping of brain activity by automated volume analysis of immediate early genes. Cell, 165(7), 1789–1802.
Article CAS PubMed PubMed Central Google Scholar
Ronneberger, O., Fischer, P., & Brox, T. (2015). U-net: Convolutional networks for biomedical image segmentation. In Medical Image Computing and Computer-Assisted Intervention–MICCAI 2015: 18th International Conference, Munich, Germany, October 5-9, 2015, Proceedings, Part III 18 (pp. 234–241). Springer.
Roy, D. S., Park, Y.-G., Kim, M. E., Zhang, Y., Ogawa, S. K., DiNapoli, N., Gu, X., Cho, J. H., Choi, H., Kamentsky, L., et al. (2022). Brain-wide mapping reveals that engrams for a single memory are distributed across multiple brain regions. Nature Communications, 13(1), 1799.
Article CAS PubMed PubMed Central Google Scholar
Sandler, M., Howard, A., Zhu, M., Zhmoginov, A., & Chen, L.-C. (2018). Mobilenetv2: Inverted residuals and linear bottlenecks. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (pp. 4510–4520).
Song, J. H., Choi, W., Song, Y.-H., Kim, J.-H., Jeong, D., Lee, S.-H., & Paik, S.-B. (2020). Precise mapping of single neurons by calibrated 3D reconstruction of brain slices reveals topographic projection in mouse visual cortex. Cell Reports, 31(8), 107682.
Article CAS PubMed Google Scholar
Tappan, S. J., Eastwood, B. S., O’Connor, N., Wang, Q., Ng, L., Feng, D., Hooks, B. M., Gerfen, C. R., Hof, P. R., Schmitz, C., et al. (2019). Automatic navigation system for the mouse brain. Journal of Comparative Neurology, 527(13), 2200–2211.
Tward, D., Li, X., Huo, B., Lee, B., Mitra, P., & Miller, M. (2019). 3D mapping of serial histology sections with anomalies using a novel robust deformable registration algorithm. In Multimodal Brain Image Analysis and Mathematical Foundations of Computational Anatomy: 4th International Workshop, MBIA 2019, and 7th International Workshop, MFCA 2019, Held in Conjunction with MICCAI 2019, Shenzhen, China, October 17, 2019, Proceedings (pp. 162–173). Springer.
Wang, Q., Ding, S.-L., Li, Y., Royall, J., Feng, D., Lesnar, P., Graddis, N., Naeemi, M., Facer, B., Ho, A., et al. (2020). The Allen mouse brain common coordinate framework: A 3D reference atlas. Cell, 181(4), 936–953.
Article CAS PubMed PubMed Central Google Scholar
Wang, Y., Li, Q., Liu, L., Zhou, Z., Ruan, Z., Kong, L., Li, Y., Wang, Y., Zhong, N., Chai, R., et al. (2019). Teravr empowers precise reconstruction of complete 3-D neuronal morphology in the whole brain. Nature Communications, 10(1), 3474.
Article PubMed PubMed Central Google Scholar
Wang, S., Niu, K., Chen, L., & Rao, X. (2022). Method for counting labeled neurons in mouse brain regions based on image representation and registration. Medical & Biological Engineering & Computing, 60(2), 487–500.
Wang, X., Zeng, W., Yang, X., Zhang, Y., Fang, C., Zeng, S., Han, Y., & Fei, P. (2021). Bi-channel image registration and deep-learning segmentation (birds) for efficient, versatile 3D mapping of mouse brain. Elife, 10, 63455.
Xiong, J., Ren, J., Luo, L., & Horowitz, M. (2018). Mapping histological slice sequences to the Allen mouse brain atlas without 3D reconstruction. Frontiers in Neuroinformatics, 12, 93.
留言 (0)