BrainGlobe publications#
Brainreg & brainglobe-segmentation (formerly brainreg-segment):
Tyson, A. L., Vélez-Fort, M., Rousseau, C. V., Cossell, L., Tsitoura, C., Lenzi, S. C., Obenhaus, H. A., Claudi, F., Branco, T., Margrie, T. W. (2022) “Accurate determination of marker location within whole-brain microscopy images” Scientific Reports, doi.org/10.1038/s41598-021-04676-9
3D cell detection:
Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M., Margrie, T. W. (2021) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets” PLOS Computational Biology 17(5): e1009074. doi.org/10.1371/journal.pcbi.1009074
Brainrender:
Claudi, F., Tyson, A. L., Petrucco, L., Margrie, T.W., Portugues, R., Branco, T. (2021) “Visualizing anatomically registered data with Brainrender” eLife 2021;10:e65751 doi.org/10.7554/eLife.65751
BrainGlobe Atlas API:
Claudi, F., Petrucco, L., Tyson, A. L., Branco, T., Margrie, T. W., Portugues, R. (2020) “BrainGlobe Atlas API: a common interface for neuroanatomical atlases” Journal of Open Source Software, 5(54), 2668 doi.org/10.21105/joss.02668
Publications citing BrainGlobe#
This list is automatically generated from Google Scholar
AlSubaie, R., Wee, R. W., Ritoux, A., Mishchanchuk, K., Passlack, J., Regester, D., & MacAskill, A. F. (2021). Control of parallel hippocampal output pathways by amygdalar long-range inhibition. Elife, 10, e74758.
An, X., Matho, K., Li, Y., Mohan, H., Xu, X. H., Whishaw, I. Q., Kepecs, A., & Huang, Z. J. (2022). A cortical circuit for orchestrating oromanual food manipulation. BioRxiv, 2022–12.
Argunşah, A. Ö., Erdil, E., Ghani, M. U., Ramiro-Cortés, Y., Hobbiss, A. F., Karayannis, T., Çetin, M., Israely, I., & Ünay, D. (2022). An interactive time series image analysis software for dendritic spines. Scientific Reports, 12(1), 12405.
Arshadi, C., Günther, U., Eddison, M., Harrington, K. I., & Ferreira, T. A. (2021). SNT: a unifying toolbox for quantification of neuronal anatomy. Nature Methods, 18(4), 374–377.
Athey, T. L., Wright, M. A., Pavlovic, M., Chandrashekhar, V., Deisseroth, K., Miller, M. I., & Vogelstein, J. T. (2023). Brainline: An open pipeline for connectivity analysis of heterogeneous whole-brain fluorescence volumes. Neuroinformatics, 21(4), 637–639.
Bao, R., Al-Shakarji, N. M., Bunyak, F., & Palaniappan, K. (2021). Dmnet: Dual-stream marker guided deep network for dense cell segmentation and lineage tracking. Proceedings of the IEEE/CVF International Conference on Computer Vision, 3361–3370.
Beyer, J., Troidl, J., Boorboor, S., Hadwiger, M., Kaufman, A., & Pfister, H. (2022). A survey of visualization and analysis in high-resolution connectomics. Computer Graphics Forum, 41(3), 573–607.
Bhatia, H. S., Brunner, A.-D., Öztürk, F., Kapoor, S., Rong, Z., Mai, H., Thielert, M., Ali, M., Al-Maskari, R., Paetzold, J. C., & others. (2022). Spatial proteomics in three-dimensional intact specimens. Cell, 185(26), 5040–5058.
(BICCN), B. I. C. C. N., Adkins, R. S., Aldridge, A. I., Allen, S., Ament, S. A., An, X., Armand, E., Ascoli, G. A., Bakken, T. E., Bandrowski, A., & others. (2020). A multimodal cell census and atlas of the mammalian primary motor cortex. Biorxiv, 2020–10.
Bimbard, C, Takács, F., Fabre, J., Melin, M., O’Neill, N., Robacha, M., Street, J., van Beest, E., Churchland, A., Harris, K., & others. (2023). Reusable, flexible, and lightweight chronic implants for Neuropixels probes. BioRxiv.
Bimbard, Célian, Sit, T. P., Lebedeva, A., Reddy, C. B., Harris, K. D., & Carandini, M. (2023). Behavioral origin of sound-evoked activity in mouse visual cortex. Nature Neuroscience, 26(2), 251–258.
Bimbard, Célian, Takács, F., Catarino, J., Fabre, J., Gupta, S., Lenzi, S., Melin, M., O’Neill, N., Robacha, M., Street, J., & others. (2023). An adaptable, reusable, and light implant for chronic Neuropixels probes. BioRxiv.
Birman, D., Yang, K. J., West, S. J., Karsh, B., Browning, Y., Laboratory, I. B., Siegle, J. H., & Steinmetz, N. A. (2023). Pinpoint: trajectory planning for multi-probe electrophysiology and injections in an interactive web-based 3D environment. BioRxiv.
Blackmore, M., Batsel, E., & Tsoulfas, P. (2021). Widening spinal injury research to consider all supraspinal cell types: Why we must and how we can. Experimental Neurology, 346, 113862.
Blixhavn, C. H., Reiten, I., Kleven, H., Øvsthus, M., Yates, S. C., Schlegel, U., Puchades, M. A., Schmid, O., Bjaalie, J. G., Bjerke, I. E., & others. (2024). The Locare workflow: representing neuroscience data locations as geometric objects in 3D brain atlases. Frontiers in Neuroinformatics, 18, 1284107.
Bonapersona, V, Schuler, H., Damsteegt, R., Adolfs, Y., Pasterkamp, R., van den Heuvel, M., Joëls, M., & Sarabdjitsingh, R. (2021). The mouse brain after foot-shock in 4D: temporal dynamics at a single-cell resolution. BioRxiv, 2021–05.
Bonapersona, Valeria, Schuler, H., Damsteegt, R., Adolfs, Y., Pasterkamp, R. J., van den Heuvel, M. P., Joëls, M., & Sarabdjitsingh, R. A. (2022). The mouse brain after foot shock in four dimensions: Temporal dynamics at a single-cell resolution. Proceedings of the National Academy of Sciences, 119(8), e2114002119.
Brown, A. P., Cossell, L., Strom, M., Tyson, A. L., Vélez-Fort, M., & Margrie, T. W. (2021). Analysis of segmentation ontology reveals the similarities and differences in connectivity onto L2/3 neurons in mouse V1. Scientific Reports, 11(1), 4983.
Buck, S. A., Rubin, S. A., Kunkhyen, T., Treiber, C. D., Xue, X., Fenno, L. E., Mabry, S. J., Sundar, V. R., Yang, Z., Shah, D., & others. (2023). Sexually dimorphic mechanisms of VGLUT-mediated protection from dopaminergic neurodegeneration. BioRxiv.
Campagner, D., Vale, R., Tan, Y. L., Iordanidou, P., Pavón Arocas, O., Claudi, F., Stempel, A. V., Keshavarzi, S., Petersen, R. S., Margrie, T. W., & others. (2020). A cortico-collicular circuit for accurate orientation to shelter during escape. BioRxiv, 2020–05.
Campagner, D., Vale, R., Tan, Y. L., Iordanidou, P., Pavón Arocas, O., Claudi, F., Stempel, A. V., Keshavarzi, S., Petersen, R. S., Margrie, T. W., & others. (2023). A cortico-collicular circuit for orienting to shelter during escape. Nature, 613(7942), 111–119.
Chalatsi, T., Fernandez, L. M., Scholler, J., Batti, L., Kolaxi, A., Restivo, L., Lüthi, A., Mameli, M., & Nikoletopoulou, V. (2022). Autophagy in parvalbumin interneurons is required for inhibitory transmission and memory via regulation of synaptic proteostasis. BioRxiv, 2022–10.
Chen, R., Liu, M., Chen, W., Wang, Y., & Meijering, E. (2023). Deep learning in mesoscale brain microscopy image analysis: A review. Computers in Biology and Medicine, 107617.
Chini, M., Hnida, M., Kostka, J. K., Chen, Y.-N., & Hanganu-Opatz, I. L. (2023). Extreme distributions in the preconfigured developing brain. BioRxiv, 2023–11.
Chini, M., Pfeffer, T., & Hanganu-Opatz, I. (2022). An increase of inhibition drives the developmental decorrelation of neural activity. Elife, 11, e78811.
Chini, M., Pfeffer, T., & Hanganu-Opatz, I. L. (2021). Developmental increase of inhibition drives decorrelation of neural activity. BioRxiv, 2021–07.
Chiu, C.-L., Clack, N., & others. (2022). Napari: A Python multi-dimensional image viewer platform for the research community. Microscopy and Microanalysis, 28(S1), 1576–1577.
Claar, L. D., Rembado, I., Kuyat, J. R., Russo, S., Marks, L. C., Olsen, S. R., & Koch, C. (2023). Cortico-thalamo-cortical interactions modulate electrically evoked EEG responses in mice. ELife, 12, RP84630.
Claudi, F., Petrucco, L., Tyson, A., Branco, T., Margrie, T., & Portugues, R. (2020). BrainGlobe Atlas API: a common interface for neuroanatomical atlases. Journal of Open Source Software, 5(54), 2668–2668.
Claudi, F., Tyson, A. L., & Branco, T. (2020). Brainrender. A Python Based Software for Visualisation of Neuroanatomical and Morphological Data. BioRxiv, 23.
Claudi, F., Tyson, A. L., Petrucco, L., Margrie, T. W., Portugues, R., & Branco, T. (2021). Visualizing anatomically registered data with brainrender. Elife, 10, e65751.
Cramer, T., Gill, R., Thirouin, Z. S., Vaas, M., Sampath, S., Martineau, F., Noya, S. B., Panzanelli, P., Sudharshan, T. J., Colameo, D., & others. (2022). Cross-talk between GABAergic postsynapse and microglia regulate synapse loss after brain ischemia. Science Advances, 8(9), eabj0112.
Culp, A. (2023). Cell Type Diversity in the Norepinephrine Signaling Network [Phdthesis]. Oregon Health.
Datta, M. S., Chen, Y., Chauhan, S., Zhang, J., De La Cruz, E. D., Gong, C., & Tomer, R. (2023). Whole-brain mapping reveals the divergent impact of ketamine on the dopamine system. Cell Reports, 42(12).
Davoudian, P. A., Shao, L.-X., & Kwan, A. C. (2023). Shared and distinct brain regions targeted for immediate early gene expression by ketamine and psilocybin. ACS Chemical Neuroscience, 14(3), 468–480.
De Filippo, R., & Schmitz, D. (2023). Differential ripple propagation along the hippocampal longitudinal axis. Elife, 12, e85488.
Dehaqani, A. A., Michelon, F., Patella, P., Petrucco, L., Piasini, E., & Iurilli, G. (2024). A mechanosensory feedback that uncouples external and self-generated sensory responses in the olfactory cortex. Cell Reports, 43(4).
Dehaqani, A. A., Michelon, F., Petrucco, L., Patella, P., Piasini, E., & Iurilli, G. (2023). A mixed mechano-olfactory code for sniff-invariant odor representations. BioRxiv, 2023–04.
Durand, S., Heller, G. R., Ramirez, T. K., Luviano, J. A., Williford, A., Sullivan, D. T., Cahoon, A. J., Farrell, C., Groblewski, P. A., Bennett, C., & others. (2023). Acute head-fixed recordings in awake mice with multiple Neuropixels probes. Nature Protocols, 18(2), 424–457.
Englund, M., James, S. S., Bottom, R., Huffman, K. J., Wilson, S. P., & Krubitzer, L. A. (2021). Comparing cortex-wide gene expression patterns between species in a common reference frame. BioRxiv, 2021–07.
Esmaeili, V., Oryshchuk, A., Asri, R., Tamura, K., Foustoukos, G., Liu, Y., Guiet, R., Crochet, S., & Petersen, C. C. (2022). Learning-related congruent and incongruent changes of excitation and inhibition in distinct cortical areas. PLoS Biology, 20(5), e3001667.
Fanton, S., & Thompson, W. H. (2023). NetPlotBrain: A Python package for visualizing networks and brains. Network Neuroscience, 7(2), 461–477.
Farrell, J. S., Hwaun, E., Dudok, B., & Soltesz, I. (2024). Neural and behavioural state switching during hippocampal dentate spikes. Nature, 1–6.
Fernholz, M. (2023). A search for functional connectivity rules in the visual thalamus and hippocampus [Phdthesis]. lmu.
Fiederling, F., Hammond, L. A., Ng, D., Mason, C., & Dodd, J. (2021). Tools for efficient analysis of neurons in a 3D reference atlas of whole mouse spinal cord. Cell Reports Methods, 1(5).
Fisher, J., Verhagen, M., Long, Z., Moissidis, M., Yan, Y., He, C., Wang, J., Micoli, E., Alastruey, C. M., Moors, R., & others. (2024). Cortical somatostatin long-range projection neurons and interneurons exhibit divergent developmental trajectories. Neuron, 112(4), 558–573.
Franceschini, A., Mazzamuto, G., Checcucci, C., Chicchi, L., Fanelli, D., Costantini, I., Passani, M. B., Silva, B. A., Pavone, F. S., & Silvestri, L. (2023). Brain-wide neuron quantification toolkit reveals strong sexual dimorphism in the evolution of fear memory. Cell Reports, 42(8).
Frankowski, J. C., Tierno, A., Pavani, S., Cao, Q., Lyon, D. C., & Hunt, R. F. (2022). Brain-wide reconstruction of inhibitory circuits after traumatic brain injury. Nature Communications, 13(1), 3417.
Fuglstad, J. G., Saldanha, P., Paglia, J., & Whitlock, J. R. (2023). Histological E-data registration in rodent brain spaces. Elife, 12, e83496.
Galloni, A. R., Ye, Z., & Rancz, E. (2022). Dendritic domain-specific sampling of long-range axons shapes feedforward and feedback connectivity of L5 neurons. Journal of Neuroscience, 42(16), 3394–3405.
Gerlei, K. Z., Brown, C. M., Sürmeli, G., & Nolan, M. F. (2021). Deep entorhinal cortex: from circuit organization to spatial cognition and memory. Trends in Neurosciences, 44(11), 876–887.
Greenstreet, F., Vergara, H. M., Pati, S., Schwarz, L., Wisdom, M., Marbach, F., Johansson, Y., Rollik, L., Moskovitz, T., Clopath, C., & others. (2022). Action prediction error: a value-free dopaminergic teaching signal that drives stable learning. BiorXiv, 2022–09.
Gruver, K. (2023). Purkinje cells converge non-randomly on neurons in the cerebellar nuclei.
Gruver, K. M., Jiao, J. W., Fields, E., Song, S., Sjöström, P. J., & Watt, A. J. (2023). Structured connectivity in the output of the cerebellar cortex. BioRxiv, 2023–03.
Guo, S., Xue, J., Liu, J., Ye, X., Guo, Y., Liu, D., Zhao, X., Xiong, F., Han, X., & Peng, H. (2022). Smart imaging to empower brain-wide neuroscience at single-cell levels. Brain Informatics, 9(1), 10.
Hagihara, K. M., Bukalo, O., Zeller, M., Aksoy-Aksel, A., Karalis, N., Limoges, A., Rigg, T., Campbell, T., Mendez, A., Weinholtz, C., & others. (2021). Intercalated amygdala clusters orchestrate a switch in fear state. Nature, 594(7863), 403–407.
Hahn, J. D., & Duckworth, C. (2023). A brain flatmap data visualization tool for mouse, rat, and human. Journal of Comparative Neurology, 531(10), 1008–1016.
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).
Jones, A. (2023). Probabilistic models for structured biomedical data [Phdthesis]. Princeton University.
Jones, A., Cai, D., Li, D., & Engelhardt, B. E. (2023). Optimizing the design of spatial genomic studies. BioRxiv.
Kaltenecker, D., Al-Maskari, R., Negwer, M., Hoeher, L., Kofler, F., Zhao, S., Todorov, M., Rong, Z., Paetzold, J. C., Wiestler, B., & others. (2024). Virtual reality-empowered deep-learning analysis of brain cells. Nature Methods, 1–10.
Kantor, B., & Ben-Ami Bartal, I. (2023). Brainways: An AI-based Tool for Automated Registration, Quantification and Generation of Brain-wide Activity Networks Based on Fluorescence in Coronal Slices. BioRxiv, 2023–05.
Keshavarzi, S., Bracey, E. F., Faville, R. A., Campagner, D., Tyson, A. L., Lenzi, S. C., Branco, T., & Margrie, T. W. (2021). The retrosplenial cortex combines internal and external cues to encode head velocity during navigation. BioRxiv, 2021–01.
Keshavarzi, S., Bracey, E. F., Faville, R. A., Campagner, D., Tyson, A. L., Lenzi, S. C., Branco, T., & Margrie, T. W. (2022). Multisensory coding of angular head velocity in the retrosplenial cortex. Neuron, 110(3), 532–543.
Kintscher, M., Kochubey, O., & Schneggenburger, R. (2023). A striatal circuit balances learned fear in the presence and absence of sensory cues. Elife, 12, e75703.
Kostka, Johanna K, & Hanganu-Opatz, I. L. (2023). Olfactory-driven beta band entrainment of limbic circuitry during neonatal development. The Journal of Physiology, 601(16), 3605–3630.
Kostka, Johanna Katharina. (2022). Olfactory entrainment of cortical-hippocampal networks during development [Phdthesis]. Staats-und Universitätsbibliothek Hamburg Carl von Ossietzky.
Lauridsen, K., Ly, A., Prévost, E. D., McNulty, C., McGovern, D. J., Tay, J. W., Dragavon, J., & Root, D. H. (2022). A semi-automated workflow for brain Slice Histology Alignment, Registration, and Cell Quantification (SHARCQ). Eneuro, 9(2).
Lenzi, S. (2021). A Role for the Tail of the Striatum in the Adaptive Control of Innate Escape Behaviour [Phdthesis]. UCL (University College London).
Li, D. (2022). Bistable Neural Dynamics Underlying Cognition and Spontaneous Activity: Computational Modeling and Empirical Analysis [Phdthesis]. Yale University.
Lowet, A. S., Zheng, Q., Meng, M., Matias, S., Drugowitsch, J., & Uchida, N. (2023). Distributional Reinforcement Learning in the Mammalian Brain. UniReps: The First Workshop on Unifying Representations in Neural Models.
Lowet, A. S., Zheng, Q., Meng, M., Matias, S., Drugowitsch, J., & Uchida, N. (2024). An opponent striatal circuit for distributional reinforcement learning. BioRxiv, 2024–01.
Lu, T., Shinozaki, M., Nagoshi, N., Nakamura, M., & Okano, H. (2022). 3D imaging of supraspinal inputs to the thoracic and lumbar spinal cord mapped by retrograde tracing and light-sheet microscopy. Journal of Neurochemistry, 162(4), 352–370.
Lupori, L., & others. (2023). Genetic and environmental factors regulating structure, function and plasticity of the visual cortex.
Lupori, L., Totaro, V., Cornuti, S., Ciampi, L., Carrara, F., Grilli, E., Viglione, A., Tozzi, F., Putignano, E., Mazziotti, R., & others. (2023). A comprehensive atlas of perineuronal net distribution and colocalization with parvalbumin in the adult mouse brain. Cell Reports, 42(7).
MacDowell, C. J., Libby, A., Jahn, C. I., Tafazoli, S., & Buschman, T. J. (2023). Multiplexed subspaces route neural activity across brain-wide networks. BioRxiv.
manuscript editors, P., coordination, A., data analysis Armand Ethan 42 Yao Zizhen 5, I., seq data ATAC-generation, processing Fang Rongxin 45 Hou Xiaomeng 10 Lucero Jacinta D. 18 Osteen Julia K. 18 Pinto-Duarte Antonio 18 Poirion Olivier 10 Preissl Sebastian 10 Wang Xinxin 10 97 97, retro-seq data Epi-generation, processing Dominguez Bertha 53 Ito-Cole Tony 1 Jacobs Matthew 1 Jin Xin 54 99 100 99 100 Lee Cheng-Ta 53 Lee Kuo-Fen 53 Miyazaki Paula Assakura 1 Pang Yan 1 Rashid Mohammad 1 Smith Jared B. 54 Vu Minh 1 Williams Elora 54, & others. (2021). A multimodal cell census and atlas of the mammalian primary motor cortex. Nature, 598(7879), 86–102.
McGovern, D. J., Polter, A. M., Prévost, E. D., Ly, A., McNulty, C. J., Rubinstein, B., & Root, D. H. (2023). Ventral tegmental area glutamate neurons establish a mu-opioid receptor gated circuit to mesolimbic dopamine neurons and regulate opioid-seeking behavior. Neuropsychopharmacology, 48(13), 1889–1900.
McKenna, K., Prasad, S., Cooper, J., King, A. M., Shahzeidi, S., Mittal, J., Zalta, M., Mittal, R., & Eshraghi, A. A. (2024). Incidence of Otolaryngological Manifestations in Individuals with Autism Spectrum Disorder: A Special Focus on Auditory Disorders. Audiology Research, 14(1), 35–61.
Mitrevica, Z., & Murray, A. J. (2023). Speed-independent modulation of locomotor gait preference by sensory feedback in mice. BioRxiv, 2023–03.
Mohan, H., An, X., Xu, X. H., Kondo, H., Zhao, S., Matho, K. S., Wang, B.-S., Musall, S., Mitra, P., & Huang, Z. J. (2023). Cortical glutamatergic projection neuron types contribute to distinct functional subnetworks. Nature Neuroscience, 26(3), 481–494.
Morimoto, M. M., Uchishiba, E., & Saleem, A. B. (2021). Organization of feedback projections to mouse primary visual cortex. IScience, 24(5).
Muñoz-Castañeda, R., Zingg, B., Matho, K. S., Chen, X., Wang, Q., Foster, N. N., Li, A., Narasimhan, A., Hirokawa, K. E., Huo, B., & others. (2021). Cellular anatomy of the mouse primary motor cortex. Nature, 598(7879), 159–166.
Negwer, M., Bosch, B., Bormann, M., Hesen, R., Lütje, L., Aarts, L., Rossing, C., Nadif Kasri, N., & Schubert, D. (2023). FriendlyClearMap: an optimized toolkit for mouse brain mapping and analysis. GigaScience, 12, giad035.
Newmaster, K. T., Kronman, F. A., Wu, Y., & Kim, Y. (2022). Seeing the forest and its trees together: implementing 3D light microscopy pipelines for cell type mapping in the mouse brain. Frontiers in Neuroanatomy, 15, 787601.
Nyberg, N., Duvelle, É., Barry, C., & Spiers, H. J. (2022). Spatial goal coding in the hippocampal formation. Neuron, 110(3), 394–422.
Paglia, J., Saldanha, P., Fuglstad, J. G., & Whitlock, J. R. (2021). TRACER: a toolkit to register and visualize anatomical coordinates in the rat brain. BioRxiv, 2021–10.
Palchaudhuri, S., Osypenko, D., Kochubey, O., & Schneggenburger, R. (2023). An insular cortex to lateral amygdala pathway in fear learning. BioRxiv, 2023–01.
Parks, D. F., Schneider, A. M., Xu, Y., Brunwasser, S. J., Funderburk, S., Thurber, D., Blanche, T., Dyer, E. L., Haussler, D., & Hengen, K. B. (2023). A non-oscillatory, millisecond-scale embedding of brain state provides insight into behavior. BioRxiv.
Patel, V. (2021). Deep Learning model to Automate the process of mapping Cancer Cells to Cell Lines & Cancer Types from Single Cell RNA-Seq Data.
Pavón Arocas, O. (2022). Biophysical properties and gene expression profile of single periaqueductal gray neurons [Phdthesis]. UCL (University College London).
Perens, J. (2021). Enabling multimodal whole-brain investigation for drug discovery.
Perens, J., & Hecksher-Sørensen, J. (2022). Digital brain maps and virtual neuroscience: An emerging role for light-sheet fluorescence microscopy in drug development. Frontiers in Neuroscience, 16, 866884.
Petrucco, L., Lavian, H., Wu, Y. K., Svara, F., Štih, V., & Portugues, R. (2023). Neural dynamics and architecture of the heading direction circuit in zebrafish. Nature Neuroscience, 26(5), 765–773.
Pochinok, I., Stöber, T. M., Triesch, J., Chini, M., & Hanganu-Opatz, I. L. (2024). A developmental increase of inhibition promotes the emergence of hippocampal ripples. Nature Communications, 15(1), 738.
Pouchelon, G., Dwivedi, D., Bollmann, Y., Agba, C. K., Xu, Q., Mirow, A. M., Kim, S., Qiu, Y., Sevier, E., Ritola, K. D., & others. (2021). The organization and development of cortical interneuron presynaptic circuits are area specific. Cell Reports, 37(6).
Prévost, E. D., Phillips, A., Lauridsen, K., Enserro, G., Rubinstein, B., Alas, D., McGovern, D. J., Ly, A., Banks, M., McNulty, C., & others. (2023). Monosynaptic inputs to ventral tegmental area glutamate and GABA co-transmitting neurons. BioRxiv.
Qian, K., Friedman, B., Takatoh, J., Wang, F., Kleinfeld, D., & Freund, Y. (2023). CellBoost: A pipeline for machine assisted annotation in neuroanatomy. BioRxiv, 2023–09.
Regev, A. (2021). A multimodal cell census and atlas of the mammalian primary motor cortex.
Ruff, K. M., Choi, Y. H., Cox, D., Ormsby, A. R., Myung, Y., Ascher, D. B., Radford, S. E., Pappu, R. V., & Hatters, D. M. (2022). Sequence grammar underlying the unfolding and phase separation of globular proteins. Molecular Cell, 82(17), 3193–3208.
Sanchez-Arias, J. C., Carrier, M., Frederiksen, S. D., Shevtsova, O., McKee, C., van der Slagt, E., Gonçalves de Andrade, E., Nguyen, H. L., Young, P. A., Tremblay, M., & others. (2021). A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy. Frontiers in Neuroanatomy, 15, 722443.
Scholler, J., Jonsson, J., Jordá-Siquier, T., Gantar, I., Batti, L., Cheeseman, B. L., Pagès, S., Sbalzarini, I. F., & Lamy, C. M. (2023). Efficient image analysis for large-scale next generation histopathology using pAPRica. BioRxiv, 2023–01.
Schweihoff, J. F. (2022). Ai-based, behavior dependent approaches for connectomic reconstruction of neuronal circuits [Phdthesis]. Universitäts-und Landesbibliothek Bonn.
Siu, P. H., Müller, E., Zerbi, V., Aquino, K., & Fulcher, B. D. (2022). Extracting dynamical understanding from neural-mass models of mouse cortex. Frontiers in Computational Neuroscience, 16, 847336.
Soltwedel, J., Suckert, T., Beyreuther, E., Schneider, M., Boucsein, M., Bodenstein, E., Nexhipi, S., Stolz-Kieslich, L., Krause, M., von Neubeck, C., & others. (2023). Slice2Volume: Fusion of multimodal medical imaging and light microscopy data of irradiation-injured brain tissue in 3D. Radiotherapy and Oncology, 182, 109591.
Szabo, G. G., Farrell, J. S., Dudok, B., Hou, W.-H., Ortiz, A. L., Varga, C., Moolchand, P., Gulsever, C. I., Gschwind, T., Dimidschstein, J., & others. (2022). Ripple-selective GABAergic projection cells in the hippocampus. Neuron, 110(12), 1959–1977.
Szelenyi, E. R., Navarrete, J. S., Murry, A. D., Zhang, Y., Girven, K. S., Kuo, L., Cline, M. M., Bernstein, M. X., Burdyniuk, M., Bowler, B., & others. (2023). An arginine-rich nuclear localization signal (ArgiNLS) strategy for streamlined image segmentation of single-cells. BioRxiv.
Takatoh, J., Park, J. H., Lu, J., Li, S., Thompson, P., Han, B.-X., Zhao, S., Kleinfeld, D., Friedman, B., & Wang, F. (2021). Constructing an adult orofacial premotor atlas in Allen mouse CCF. Elife, 10.
Takatoh, J., Prevosto, V., Thompson, P., Lu, J., Chung, L., Harrahill, A., Li, S., Zhao, S., He, Z., Golomb, D., & others. (2022). The whisking oscillator circuit. Nature, 609(7927), 560–568.
Tantirigama, M. L., Schoenherr, A., Moreno-Velasquez, L., Faiss, L., Rost, B. R., Larkum, M. E., Judkewitz, B., Stumpenhorst, K., Rivalan, M., Winter, Y., & others. (2023). Binge Feeding Promotes Appetite via Modulating Olfactory Flavor Representation. BioRxiv, 2023–10.
Taylor, D. (2023). A brainstem circuit mechanism for coordinating the head and eyes during gaze movements [Phdthesis]. University of California, San Francisco.
Terstege, D. J., & Epp, J. R. (2022). Network neuroscience untethered: brain-wide immediate early gene expression for the analysis of functional connectivity in freely behaving animals. Biology, 12(1), 34.
Terstege, D. J., Oboh, D. O., & Epp, J. R. (2022). FASTMAP: Open-source flexible atlas segmentation tool for multi-area processing of biological images. ENeuro, 9(2).
Thompson, E. (2024). Subcortical circuits for procedural learning and memory [Phdthesis]. UCL (University College London).
Tillmann, J. F. (n.d.). Ai-based, behavior dependent approaches for connectomic reconstruction of neuronal circuits [Phdthesis]. Dissertation, Bonn, Rheinische Friedrich-Wilhelms-Universität, 2022.
Toubal, I. E., Al-Shakarji, N., Cornelison, D., & Palaniappan, K. (2023). Ensemble deep learning object detection fusion for cell tracking, mitosis, and lineage. IEEE Open Journal of Engineering in Medicine and Biology.
Tran-Van-Minh, A., Ye, Z., & Rancz, E. (2023). Quantitative analysis of rabies virus-based synaptic connectivity tracing. PLoS One, 18(3), e0278053.
Tsoi, S. Y., Öncül, M., Svahn, E., Robertson, M., Bogdanowicz, Z., McClure, C., & Sürmeli, G. (2021). Telencephalic outputs from the medial entorhinal cortex are copied directly to the hippocampus. BioRxiv, 2021–03.
Tsoi, S. Y., Öncül, M., Svahn, E., Robertson, M., Bogdanowicz, Z., McClure, C., & Sürmeli, G. (2022). Telencephalic outputs from the medial entorhinal cortex are copied directly to the hippocampus. Elife, 11, e73162.
Tyson, A. L., & Margrie, T. W. (2022). Mesoscale microscopy and image analysis tools for understanding the brain. Progress in Biophysics and Molecular Biology, 168, 81–93.
Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M., & Margrie, T. W. (2021). A deep learning algorithm for 3D cell detection in whole mouse brain image datasets. PLoS Computational Biology, 17(5), e1009074.
Tyson, A. L., Vélez-Fort, M., Rousseau, C. V., Cossell, L., Tsitoura, C., Lenzi, S. C., Obenhaus, H. A., Claudi, F., Branco, T., & Margrie, T. W. (2022). Accurate determination of marker location within whole-brain microscopy images. Scientific Reports, 12(1), 867.
Tyson, A. L., Vélez-Fort, M., Rousseau, C. V., Cossell, L., Tsitoura, C., Obenhaus, H. A., Claudi, F., Lenzi, S. C., Branco, T., & Margrie, T. W. (2021). Tools for accurate post hoc determination of marker location within whole-brain microscopy images. BioRxiv, 2021–05.
Vohra, S. K., Harth, P., Isoe, Y., Bahl, A., Fotowat, H., Engert, F., Hege, H.-C., & Baum, D. (2023). A visual interface for exploring hypotheses about neural circuits. IEEE Transactions on Visualization and Computer Graphics.
Wagner, R., & Rohr, K. (2022). Cellcentroidformer: Combining self-attention and convolution for cell detection. Annual Conference on Medical Image Understanding and Analysis, 212–222.
Walker, L. A., Williams, J. S., Li, Y., Roossien, D. H., Lee, W. J., Michki, N. S., & Cai, D. (2022). ngauge: Integrated and extensible neuron morphology analysis in python. Neuroinformatics, 20(3), 755–764.
Wang, L.-W., Wu, Y.-L., Lee, C.-L., Cheng, C.-C., Lu, K.-Y., Tsai, J.-H., Lin, Y.-H., Hsu, C.-H., Kuo, T.-H., & Chu, L.-A. (2023). A Weakly Supervised U-Net Model for Precise Whole Brain Immunolabeled Cell Detection. BioRxiv, 2023–03.
Wang, Z., Romanski, A., Mehra, V., Wang, Y., Brannigan, M., Campbell, B. C., Petsko, G. A., Tsoulfas, P., & Blackmore, M. G. (2022). Brain-wide analysis of the supraspinal connectome reveals anatomical correlates to functional recovery after spinal injury. Elife, 11, e76254.
Wang, Z., Romanski, A., Mehra, V., Wang, Y., Campbell, B. C., Petsko, G. A., Tsoulfas, P., & Blackmore, M. (2021). Brain-wide quantification of the supraspinal connectome. BioRxiv, 2021–06.
Weiler, S., Rahmati, V., Isstas, M., Wutke, J., Stark, A. W., Franke, C., Graf, J., Geis, C., Witte, O. W., Hübener, M., & others. (2024). A primary sensory cortical interareal feedforward inhibitory circuit for tacto-visual integration. Nature Communications, 15(1), 3081.
Weiler, S., Teichert, M., & Margrie, T. W. (2024). Layer 6 corticocortical cells dominate the anatomical organization of intra and interhemispheric feedback. BioRxiv, 2024–05.
Wilde, M., Constantin, L., Thorne, P. R., Montgomery, J. M., Scott, E. K., & Cheyne, J. E. (2022). Auditory processing in rodent models of autism: a systematic review. Journal of Neurodevelopmental Disorders, 14(1), 48.
Xie, Z., Wang, M., Liu, Z., Shang, C., Zhang, C., Sun, L., Gu, H., Ran, G., Pei, Q., Ma, Q., & others. (2021). Transcriptomic encoding of sensorimotor transformation in the midbrain. Elife, 10, e69825.
Yang, W., Kanodia, H., & Arber, S. (2023). Structural and functional map for forelimb movement phases between cortex and medulla. Cell, 186(1), 162–177.
Zahler, S. H., Taylor, D. E., Wright, B. S., Wong, J. Y., Shvareva, V. A., Park, Y. A., & Feinberg, E. H. (2023). Hindbrain modules differentially transform activity of single collicular neurons to coordinate movements. Cell, 186(14), 3062–3078.
Zhang, Y., Ackels, T., Pacureanu, A., Zdora, M.-C., Bonnin, A., Schaefer, A. T., & Bosch, C. (2022). Sample preparation and warping accuracy for correlative multimodal imaging in the mouse olfactory bulb using 2-photon, synchrotron x-ray and volume electron microscopy. Frontiers in Cell and Developmental Biology, 10, 880696.
Zhou, H., Li, Y., Wen, W., Yang, H., Ma, Y., & Chen, M. (2024). Accurately 3D neuron localization using 2D conv-LSTM super-resolution segmentation network. IET Image Processing, 18(2), 535–547.
Zhu, Y., Wang, G., Kolluru, C., Gu, Y., Gao, H., Zhang, J., Wang, Y., Wilson, D. L., Zhu, X., Flask, C. A., & others. (n.d.). This manuscript was submitted to JCBFM for review on Nov 3, 2022.
Zhu, Y., Wang, G., Kolluru, C., Gu, Y., Gao, H., Zhang, J., Wang, Y., Wilson, D. L., Zhu, X., Flask, C. A., & others. (2023). Transport pathways and kinetics of cerebrospinal fluid tracers in mouse brain observed by dynamic contrast-enhanced MRI. Scientific Reports, 13(1), 13882.
Zhukovskaya, A., Zimmerman, C. A., Willmore, L., Janarthanan, S. N., Falkner, A. L., & Witten, I. B. (2023). Differences in an aversive teaching signal produce brainwide and behavioral substrates of susceptibility. BioRxiv, 2023–11.
Zimmerman, C. A., Pan-Vazquez, A., Wu, B., Keppler, E. F., Guthman, E. M., Fetcho, R. N., Bolkan, S. S., McMannon, B., Lee, J., Hoag, A. T., & others. (2023). A neural mechanism for learning from delayed postingestive feedback. BioRxiv.