Abbott, L. F., Bock, D. D., Callaway, E. M., Denk, W., Dulac, C., Fairhall, A. L., Fiete, I., Harris, K. M., Helmstaedter, M., Jain, V., Kasthuri, N., LeCun, Y., Lichtman, J. W., Littlewood, P. B., Luo, L., Maunsell, J. H., Reid, R. C., Rosen, B. R., Rubin, G. M., … Van Essen, D. C. (2020). The mind of a mouse. Cell, 182(6), 1372–1376.

Article  CAS  PubMed  Google Scholar 

Acsády, L. (2022). Organization of thalamic inputs. The thalamus (Halassa M, ed). Cambridge: Cambridge University Press. [Google Scholar].

Amato, S. P., Pan, F., Schwartz, J., & Ragan, T. M. (2016). Whole brain imaging with serial two-photon tomography. Frontiers in Neuroanatomy, 10. Technology Report.

Bakker, R., Tiesinga, P., & Kötter, R. (2015). The scalable brain atlas: Instant web-based access to public brain atlases and related content. Neuroinformatics, 13(3), 353:366.

Berg, S., Kutra, D., Kroeger, T., Straehle, C. N., Kausler, B. X., Haubold, C., Schiegg, M., Ales, J., Beier, T., Rudy, M., Eren, K., Cervantes, J. I., Xu, B., Beuttenmueller, F., Wolny, A., Zhang, C., Koethe, U., Hamprecht, F. A., & Kreshuk, A. (2019). ilastik: interactive machine learning for (bio)image analysis. Nature Methods, 16(12), 1226–1232.

Article  CAS  PubMed  Google Scholar 

Bienkowski, M. S., Bowman, I., Song, M. Y., Gou, L., Ard, T., Cotter, K., Zhu, M., Benavidez, N. L., Yamashita, S., Abu-Jaber, J., Azam, S., Lo, D., Foster, N. N., Hintiryan, H., & Dong, H.-W. (2018). Integration of gene expression and brain-wide connectivity reveals the multiscale organization of mouse hippocampal networks. Nature Neuroscience, 21(11), 1628–1643.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bradski, G. (2000). The OpenCV Library. Dr. Dobb’s Journal of Software Tools.

Buzsáki, G., Anastassiou, C. A., & Koch, C. (2012). The origin of extracellular fields and currents – eeg, ecog, lfp and spikes. Nature Reviews Neuroscience, 13(6), 407–420.

Article  PubMed  PubMed Central  Google Scholar 

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, page 2022.04.28.489953.

Casas-Torremocha, D., Rubio-Teves, M., Hoerder-Suabedissen, A., Hayashi, S., Prensa, L., Molnár, Z., Porrero, C., & Clasca, F. (2022). A combinatorial input landscape in the “higher-order relay’’ posterior thalamic nucleus. Journal of Neuroscience, 42(41), 7757–7781.

CAS  PubMed  Google Scholar 

Chon, U., Vanselow, D. J., Cheng, K. C., & Kim, Y. (2019). Enhanced and unified anatomical labeling for a common mouse brain atlas. Nature Communications, 10(1), 5067.

Article  PubMed  PubMed Central  Google Scholar 

Clascá, F. (2022). Thalamic output pathways. The Thalamus. Cambridge University Press, Cambridge, UK, page 45–70.

Dufour, A., Seibt, J., Passante, L., Depaepe, V., Ciossek, T., Frisén, J., Kullander, K., Flanagan, J. G., Polleux, F., & Vanderhaeghen, P. (2003). Area specificity and topography of thalamocortical projections are controlled by ephrin/eph genes. Neuron, 39(3), 453–465.

Article  CAS  PubMed  Google Scholar 

Gong, H., Xu, D., Yuan, J., Li, X., Guo, C., Peng, J., Li, Y., Schwarz, L. A., Li, A., Hu, B., Xiong, B., Sun, Q., Zhang, Y., Liu, J., Zhong, Q., Xu, T., Zeng, S., & Luo, Q. (2016). High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level. Nature Communications, 7(1), 12142.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Grienberger, C., & Konnerth, A. (2012). Imaging calcium in neurons. Neuron, 73(5), 862–885.

Article  CAS  PubMed  Google Scholar 

Haidarliu, S., & Ahissar, E. (2001). Size gradients of barreloids in the rat thalamus. Journal of Comparative Neurology, 429(3), 372–387.

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  PubMed Central  Google Scholar 

Harris, J. A., Oh, S. W., & Zeng, H. (2012). Adeno-associated viral vectors for anterograde axonal tracing with fluorescent proteins in nontransgenic and cre driver mice. Current Protocols in Neuroscience, 59(1), 1–20.

Article  CAS  Google Scholar 

Hill, C. L., & Stephens, G. J. (2021). An Introduction to Patch Clamp Recording, pages 1–19. Springer US, New York, NY.

Hua, Y., Loomba, S., Pawlak, V., Voit, K.-M., Laserstein, P., Boergens, K. M., Wallace, D. J., Kerr, J. N., & Helmstaedter, M. (2022). Connectomic analysis of thalamus-driven disinhibition in cortical layer 4. Cell Reports, 41(2), 111476.

Article  CAS  PubMed  Google Scholar 

Ito, M. (1988). Response properties and topography of vibrissa-sensitive vpm neurons in the rat. Journal of Neurophysiology, 60(4), 1181–1197. PMID: 3193152.

Article  CAS  PubMed  Google Scholar 

Jeong, M., Kim, Y., Kim, J., Ferrante, D. D., Mitra, P. P., Osten, P., & Kim, D. (2016). Comparative three-dimensional connectome map of motor cortical projections in the mouse brain. Scientific Reports, 6(1), 20072.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jones, E. G. (2007). The thalamus. Cambridge University Press, Cambridge, UK, 2nd ed edition.

Kaufman, L., & Rousseeuw, P. (1990). Partitioning Around Medoids (Program PAM), pages 68–125. Wiley Series in Probability and Statistics. John Wiley & Sons, Ltd.

Kim, Y., Yang, G. R., Pradhan, K., Venkataraju, K. U., Bota, M., García del Molino, L. C., Fitzgerald, G., Ram, K., He, M., Levine, J. M., Mitra, P., Huang, Z. J., Wang, X.-J., & Osten, P. (2017). Brain-wide maps reveal stereotyped cell-type-based cortical architecture and subcortical sexual dimorphism. Cell, 171(2), 456-469.e22.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Knox, J. E., Harris, K. D., Graddis, N., & Whitesell, J. D. (2018). High resolution data-driven model of the mouse connectome network neuroscience. Neuroscience, 3(1), 217–236.

Google Scholar 

Land, P. W., & Simons, D. J. (1985). Cytochrome oxidase staining in the rat smi barrel cortex. Journal of Comparative Neurology, 238(2), 225–235.

Article  CAS  PubMed  Google Scholar 

Lein, E. S., et al. (2007). Genome-wide atlas of gene expression in the adult mouse brain. Nature, 445, 168–176.

Article  CAS  PubMed  Google Scholar 

Liu, Y., Foustoukos, G., Crochet, S., & Petersen, C. C. (2022). Axonal and dendritic morphology of excitatory neurons in layer 2/3 mouse barrel cortex imaged through whole-brain two-photon tomography and registered to a digital brain atlas. Frontiers in Neuroanatomy, 15.

Meijering, E. H., Niessen, W. J., & Viergever, M. A. (2001). Quantitative evaluation of convolution-based methods for medical image interpolation. Medical Image Analysis, 5(2), 111–126.

Article  CAS  PubMed  Google Scholar 

Mukherjee, A., Bajwa, N., Lam, N. H., Porrero, C., Clasca, F., & Halassa, M. M. (2020). Variation of connectivity across exemplar sensory and associative thalamocortical loops in the mouse. eLife, 9, e62554.

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

Article  CAS  PubMed  PubMed Central  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.

Article  PubMed  Google Scholar 

Paxinos, G., & Franklin, K. B. J. (2019). Paxinos and Franklin’s The mouse brain in stereotaxic coordinates. Academic Press, an imprint of Elsevier, London, fifth edition.

Peng, H., Xie, P., Liu, L., Kuang, X., Wang, Y., Qu, L., Gong, H., Jiang, S., Li, A., Ruan, Z., Ding, L., Yao, Z., Chen, C., Chen, M., Daigle, T. L., Dalley, R., Ding, Z., Duan, Y., Feiner, A., … Zeng, H. (2021). Morphological diversity of single neurons in molecularly defined cell types. Nature, 598(7879), 174–181.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pierret, T., Lavallée, P., & Deschênes, M. (2000). Parallel streams for the relay of vibrissal information through thalamic barreloids. Journal of Neuroscience, 20(19), 7455–7462.

Article  CAS  PubMed  Google Scholar 

Potjans, T. C., & Diesmann, M. (2012). The cell-type specific cortical microcircuit: relating structure and activity in a full-scale spiking network model. Cereb Cortex, 24(3), 785–806.

Article  PubMed  PubMed Central  Google Scholar 

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), e0216796.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Saporta, S., & Kruger, L. (1977). The organization of thalamocortical relay neurons in the rat ventrobasal complex studied by the retrograde transport of horseradish peroxidase. Journal of Comparative Neurology, 174(2), 187–208.

Article  CAS  PubMed  Google Scholar 

Sherman, S. M. (2016). Thalamus plays a central role in ongoing cortical functioning. Nature Neuroscience, 19(4), 533–541.

Article  CAS  PubMed  Google Scholar 

Shu, S., Ju, G., & Fan, L. (1988). The glucose oxidase-dab-nickel method in peroxidase histochemistry of the nervous system. Neuroscience Letters, 85(2), 169–171.

Article  CAS  PubMed  Google Scholar 

Sobolewski, A., Swiejkowski, D. A., Wróbel, A., & Kublik, E. (2011). The 5–12hz oscillations in the barrel cortex of awake rats - sustained attention during behavioral idling? Clinical Neurophysiology, 122(3), 483–489.

Article  PubMed  Google Scholar 

Spreafico, R., Barbaresi, P., Weinberg, R. J., & Rustioni, A. (1987). Sii-projecting neurons in the rat thalamus: A single- and double-retrograde-tracing study. Somatosensory Research, 4(4), 359–375.

Article  CAS  PubMed  Google Scholar 

Stelzer, E. H. K., Strobl, F., Chang, B.-J., Preusser, F., Preibisch, S., McDole, K., & Fiolka, R. (2021). Light sheet fluorescence microscopy. Nature Reviews Methods Primers, 1(1), 73.

Article  CAS  Google Scholar