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For: Puchades MA, Csucs G, Ledergerber D, Leergaard TB, Bjaalie JG. Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PLoS One 2019;14:e0216796. [PMID: 31141518 DOI: 10.1371/journal.pone.0216796] [Cited by in Crossref: 35] [Cited by in F6Publishing: 45] [Article Influence: 8.8] [Reference Citation Analysis]
Number Citing Articles
1 Davoudian PA, Shao LX, Kwan AC. Shared and Distinct Brain Regions Targeted for Immediate Early Gene Expression by Ketamine and Psilocybin. ACS Chem Neurosci 2023;14:468-80. [PMID: 36630309 DOI: 10.1021/acschemneuro.2c00637] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
2 Joshi DC, Patel SS, Pillai B. Spatial transcriptomics. Transcriptome Profiling 2023. [DOI: 10.1016/b978-0-323-91810-7.00019-4] [Reference Citation Analysis]
3 Terstege DJ, Epp JR. Network Neuroscience Untethered: Brain-Wide Immediate Early Gene Expression for the Analysis of Functional Connectivity in Freely Behaving Animals. Biology (Basel) 2022;12. [PMID: 36671727 DOI: 10.3390/biology12010034] [Reference Citation Analysis]
4 Yao Y, Barger Z, Saffari Doost M, Tso CF, Darmohray D, Silverman D, Liu D, Ma C, Cetin A, Yao S, Zeng H, Dan Y. Cardiovascular baroreflex circuit moonlights in sleep control. Neuron 2022;110:3986-3999.e6. [PMID: 36170850 DOI: 10.1016/j.neuron.2022.08.027] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
5 Lopes MM, Paysan J, Rino J, Lopes SM, Pereira de Almeida L, Cortes L, Nobre RJ. A new protocol for whole-brain biodistribution analysis of AAVs by tissue clearing, light-sheet microscopy and semi-automated spatial quantification. Gene Ther 2022;29:665-79. [PMID: 36316447 DOI: 10.1038/s41434-022-00372-z] [Reference Citation Analysis]
6 Chen X, Fischer S, Zhang A, Gillis J, Zador AM. Modular cell type organization of cortical areas revealed by in situ sequencing.. [DOI: 10.1101/2022.11.06.515380] [Cited by in F6Publishing: 1] [Reference Citation Analysis]
7 Leergaard TB, Bjaalie JG. Atlas-based data integration for mapping the connections and architecture of the brain. Science 2022;378:488-492. [DOI: 10.1126/science.abq2594] [Reference Citation Analysis]
8 BICCN Data Ecosystem Collaboration, Hawrylycz MJ, Martone ME, Hof PR, Lein ES, Regev A, Ascoli GAA, Bjaalie JG, Dong H, Ghosh SS, Gillis J, Hertzano R, Haynor DR, Kim Y, Liu Y, Miller JA, Mitra PP, Mukamel E, Osumi-sutherland D, Peng H, Ray PL, Sanchez R, Ropelewski A, Scheuermann RH, Tan SZK, Tickle T, Tilgner H, Varghese M, Wester B, White O, Aevermann B, Allemang D, Ament S, Athey TL, Baker PM, Baker C, Baker KS, Bandrowski A, Bishwakarma P, Carr A, Chen M, Choudhury R, Cool J, Creasy H, D'orazi F, Degatano K, Dichter B, Ding S, Dolbeare T, Ecker JR, Fang R, Fillion-robin J, Fliss TP, Gee J, Gillespie T, Gouwens N, Halchenko YO, Harris N, Herb BR, Hintiryan H, Hood G, Horvath S, Jarecka D, Jiang S, Khajouei F, Kiernan EA, Kir H, Kruse L, Lee C, Lelieveldt B, Li Y, Liu H, Markuhar A, Mathews J, Mathews KL, Miller MI, Mollenkopf T, Mufti S, Mungall CJ, Ng L, Orvis J, Puchades MA, Qu L, Receveur JP, Ren B, Sjoquist N, Staats B, Thompson CL, Tward D, van Velthoven CTJ, Wang Q, Xie F, Xu H, Yao Z, Yun Z, Zeng H, Zhang G, Zhang YR, Zheng JW, Zingg B. The BRAIN Initiative Cell Census Network Data Ecosystem: A User’s Guide.. [DOI: 10.1101/2022.10.26.513573] [Reference Citation Analysis]
9 Pinto R, Matula J, Gomez-Lazaro M, Sousa M, Lobo A, Zikmund T, Kaiser J, Gomes JR. High-resolution micro-CT for 3D infarct characterization and segmentation in mice stroke models. Sci Rep 2022;12:17471. [PMID: 36261475 DOI: 10.1038/s41598-022-21494-9] [Reference Citation Analysis]
10 Jo Y, Lee SM, Jung T, Park G, Lee C, Im GH, Lee S, Park JS, Oh C, Kook G, Kim H, Kim S, Lee BC, Suh GSB, Kim SG, Kim J, Lee HJ. General-Purpose Ultrasound Neuromodulation System for Chronic, Closed-Loop Preclinical Studies in Freely Behaving Rodents. Adv Sci (Weinh) 2022;9:e2202345. [PMID: 36259285 DOI: 10.1002/advs.202202345] [Reference Citation Analysis]
11 Bokiniec P, Whitmire CJ, Leva TM, Poulet JFA. Brain-wide connectivity map of mouse thermosensory cortices. Cereb Cortex 2022:bhac386. [PMID: 36255325 DOI: 10.1093/cercor/bhac386] [Reference Citation Analysis]
12 Botros P, Vendrell-llopis N, Costa RM, Carmena JM. A neural model of proximity to reward.. [DOI: 10.1101/2022.10.03.510669] [Reference Citation Analysis]
13 Timme NM, Ma B, Linsenbardt D, Cornwell E, Galbari T, Lapish CC. Compulsive alcohol drinking in rodents is associated with altered representations of behavioral control and seeking in dorsal medial prefrontal cortex. Nat Commun 2022;13:3990. [PMID: 35810193 DOI: 10.1038/s41467-022-31731-4] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 3.0] [Reference Citation Analysis]
14 Bokiniec P, Whitmire CJ, Leva TM, Poulet JF. Brain-wide connectivity map of mouse thermosensory cortices.. [DOI: 10.1101/2022.06.29.498101] [Reference Citation Analysis]
15 Ham GX, Augustine GJ. Topologically Organized Networks in the Claustrum Reflect Functional Modularization. Front Neuroanat 2022;16:901807. [DOI: 10.3389/fnana.2022.901807] [Reference Citation Analysis]
16 Grady FS, Graff SA, Aldridge GM, Geerling JC. BoutonNet: an automatic method to detect anterogradely labeled presynaptic boutons in brain tissue sections. Brain Struct Funct. [DOI: 10.1007/s00429-022-02504-y] [Reference Citation Analysis]
17 Carey H, Pegios M, Martin L, Saleeba C, Turner A, Everett N, Puchades M, Bjaalie J, Mcmullan S. DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas.. [DOI: 10.1101/2022.04.28.489953] [Reference Citation Analysis]
18 Szabo GG, Farrell JS, Dudok B, Hou WH, Ortiz AL, Varga C, Moolchand P, Gulsever CI, Gschwind T, Dimidschstein J, Capogna M, Soltesz I. Ripple-selective GABAergic projection cells in the hippocampus. Neuron 2022:S0896-6273(22)00310-5. [PMID: 35489331 DOI: 10.1016/j.neuron.2022.04.002] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
19 Bjerke IE, Cullity ER, Kjelsberg K, Charan KM, Leergaard TB, Kim JH. DOPAMAP, high-resolution images of dopamine 1 and 2 receptor expression in developing and adult mouse brains. Sci Data 2022;9:175. [PMID: 35440585 DOI: 10.1038/s41597-022-01268-8] [Reference Citation Analysis]
20 Jovanovic P, Wang Y, Vit JP, Novinbakht E, Morones N, Hogg E, Tagliati M, Riera CE. Sustained chemogenetic activation of locus coeruleus norepinephrine neurons promotes dopaminergic neuron survival in synucleinopathy. PLoS One 2022;17:e0263074. [PMID: 35316276 DOI: 10.1371/journal.pone.0263074] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
21 Sadeghi M, Neto P, Ramos-prats A, Castaldi F, Paradiso E, Mahmoodian N, Ferraguti F, Goebel G. Automatic 2D to 3D localization of histological mouse brain sections in the reference atlas using deep learning. Medical Imaging 2022: Image Processing 2022. [DOI: 10.1117/12.2604231] [Reference Citation Analysis]
22 Bumgarner JR, Nelson RJ. Open-source analysis and visualization of segmented vasculature datasets with VesselVio. Cell Reports Methods 2022;2:100189. [DOI: 10.1016/j.crmeth.2022.100189] [Cited by in Crossref: 2] [Article Influence: 2.0] [Reference Citation Analysis]
23 Davoudian PA, Shao L, Kwan AC. Shared and distinct brain regions targeted for immediate early gene expression by ketamine and psilocybin.. [DOI: 10.1101/2022.03.18.484437] [Cited by in Crossref: 3] [Cited by in F6Publishing: 4] [Article Influence: 3.0] [Reference Citation Analysis]
24 Tocco C, Øvsthus M, Bjaalie JG, Leergaard TB, Studer M. The topography of corticopontine projections is controlled by postmitotic expression of the area-mapping gene Nr2f1. Development 2022;149:dev200026. [PMID: 35262177 DOI: 10.1242/dev.200026] [Cited by in Crossref: 1] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
25 Pinto R, Matula J, Gomez-lazaro M, Sousa M, Zikmund T, Kaiser J, Gomes JR. High resolution micro-CT imaging in mice stroke models: from 3D detailed infarct characterization to automatic area segmentation.. [DOI: 10.1101/2022.02.02.478782] [Reference Citation Analysis]
26 Kim GT, Bahn S, Kim N, Choi JH, Kim JS, Rah JC. Efficient and Accurate Synapse Detection With Selective Structured Illumination Microscopy on the Putative Regions of Interest of Ultrathin Serial Sections. Front Neuroanat 2021;15:759816. [PMID: 34867216 DOI: 10.3389/fnana.2021.759816] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.5] [Reference Citation Analysis]
27 Piluso S, Souedet N, Jan C, Clouchoux C, Delzescaux T. Automated Atlas-based Segmentation of Single Coronal Mouse Brain Slices using Linear 2D-2D Registration. 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC) 2021. [DOI: 10.1109/embc46164.2021.9631097] [Reference Citation Analysis]
28 Fiederling F, Hammond LA, Ng D, Mason C, Dodd J. Tools for efficient analysis of neurons in a 3D reference atlas of whole mouse spinal cord. Cell Rep Methods 2021;1:100074. [PMID: 34661190 DOI: 10.1016/j.crmeth.2021.100074] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
29 Kim N, Bahn S, Choi JH, Kim JS, Rah JC. Synapses from the Motor Cortex and a High-Order Thalamic Nucleus are Spatially Clustered in Proximity to Each Other in the Distal Tuft Dendrites of Mouse Somatosensory Cortex. Cereb Cortex 2021:bhab236. [PMID: 34355731 DOI: 10.1093/cercor/bhab236] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.5] [Reference Citation Analysis]
30 McDonald MW, Jeffers MS, Filadelfi M, Vicencio A, Heidenreich G, Wu J, Silasi G. Localizing Microemboli within the Rodent Brain through Block-Face Imaging and Atlas Registration. eNeuro 2021;8:ENEURO. [PMID: 34272259 DOI: 10.1523/ENEURO.0216-21.2021] [Reference Citation Analysis]
31 Song JH, Choi W, Song YH, Kim JH, Jeong D, Lee SH, Paik SB. Precise Mapping of Single Neurons by Calibrated 3D Reconstruction of Brain Slices Reveals Topographic Projection in Mouse Visual Cortex. Cell Rep 2020;31:107682. [PMID: 32460016 DOI: 10.1016/j.celrep.2020.107682] [Cited by in Crossref: 16] [Cited by in F6Publishing: 17] [Article Influence: 8.0] [Reference Citation Analysis]
32 Tocco C, Øvsthus M, Bjaalie JG, Leergaard TB, Studer M. Topography of corticopontine projections is controlled by postmitotic expression of the area-mapping gene Nr2f1.. [DOI: 10.1101/2021.05.10.443413] [Reference Citation Analysis]
33 Whilden CM, Chevée M, An SY, Brown SP. The synaptic inputs and thalamic projections of two classes of layer 6 corticothalamic neurons in primary somatosensory cortex of the mouse. J Comp Neurol 2021. [PMID: 33908623 DOI: 10.1002/cne.25163] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.5] [Reference Citation Analysis]
34 Timme NM, Ma B, Linsenbardt D, Cornwell E, Galbari T, Lapish C. Compulsive drinking is associated with neural activity patterns reflecting diminished behavioral control and enhanced seeking representations in dorsal medial prefrontal cortex.. [DOI: 10.1101/2021.03.15.435169] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
35 Guyon N, Zacharias LR, Fermino de Oliveira E, Kim H, Leite JP, Lopes-Aguiar C, Carlén M. Network Asynchrony Underlying Increased Broadband Gamma Power. J Neurosci 2021;41:2944-63. [PMID: 33593859 DOI: 10.1523/JNEUROSCI.2250-20.2021] [Cited by in Crossref: 17] [Cited by in F6Publishing: 21] [Article Influence: 8.5] [Reference Citation Analysis]
36 Bjerke IE, Yates SC, Laja A, Witter MP, Puchades MA, Bjaalie JG, Leergaard TB. Densities and numbers of calbindin and parvalbumin positive neurons across the rat and mouse brain. iScience 2021;24:101906. [PMID: 33385111 DOI: 10.1016/j.isci.2020.101906] [Cited by in Crossref: 13] [Cited by in F6Publishing: 15] [Article Influence: 6.5] [Reference Citation Analysis]
37 Kim S, Jo Y, Kook G, Pasquinelli C, Kim H, Kim K, Hoe HS, Choe Y, Rhim H, Thielscher A, Kim J, Lee HJ. Transcranial focused ultrasound stimulation with high spatial resolution. Brain Stimul 2021;14:290-300. [PMID: 33450428 DOI: 10.1016/j.brs.2021.01.002] [Cited by in Crossref: 15] [Cited by in F6Publishing: 12] [Article Influence: 7.5] [Reference Citation Analysis]
38 Oh SW, Son SJ, Morris JA, Choi JH, Lee C, Rah JC. Comprehensive Analysis of Long-Range Connectivity from and to the Posterior Parietal Cortex of the Mouse. Cereb Cortex 2021;31:356-78. [PMID: 32901251 DOI: 10.1093/cercor/bhaa230] [Reference Citation Analysis]
39 Conte D, Borisyuk R, Hull M, Roberts A. A simple method defines 3D morphology and axon projections of filled neurons in a small CNS volume: Steps toward understanding functional network circuitry. J Neurosci Methods 2021;351:109062. [PMID: 33383055 DOI: 10.1016/j.jneumeth.2020.109062] [Reference Citation Analysis]
40 Guyon N, Zacharias LR, de Oliveira EF, Kim H, Leite JP, Lopes-aguiar C, Carlén M. Network asynchrony underlying increased broadband gamma power.. [DOI: 10.1101/2020.08.26.265439] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.0] [Reference Citation Analysis]
41 Groeneboom NE, Yates SC, Puchades MA, Bjaalie JG. Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. Front Neuroinform 2020;14:37. [PMID: 32973479 DOI: 10.3389/fninf.2020.00037] [Cited by in Crossref: 7] [Cited by in F6Publishing: 10] [Article Influence: 2.3] [Reference Citation Analysis]
42 Allegra Mascaro AL, Falotico E, Petkoski S, Pasquini M, Vannucci L, Tort-Colet N, Conti E, Resta F, Spalletti C, Ramalingasetty ST, von Arnim A, Formento E, Angelidis E, Blixhavn CH, Leergaard TB, Caleo M, Destexhe A, Ijspeert A, Micera S, Laschi C, Jirsa V, Gewaltig MO, Pavone FS. Experimental and Computational Study on Motor Control and Recovery After Stroke: Toward a Constructive Loop Between Experimental and Virtual Embodied Neuroscience. Front Syst Neurosci 2020;14:31. [PMID: 32733210 DOI: 10.3389/fnsys.2020.00031] [Cited by in Crossref: 12] [Cited by in F6Publishing: 12] [Article Influence: 4.0] [Reference Citation Analysis]
43 Wang Q, Ding SL, Li Y, Royall J, Feng D, Lesnar P, Graddis N, Naeemi M, Facer B, Ho A, Dolbeare T, Blanchard B, Dee N, Wakeman W, Hirokawa KE, Szafer A, Sunkin SM, Oh SW, Bernard A, Phillips JW, Hawrylycz M, Koch C, Zeng H, Harris JA, Ng L. The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell 2020;181:936-953.e20. [PMID: 32386544 DOI: 10.1016/j.cell.2020.04.007] [Cited by in Crossref: 244] [Cited by in F6Publishing: 275] [Article Influence: 81.3] [Reference Citation Analysis]
44 Allegra Mascaro AL, Falotico E, Petkoski S, Pasquini M, Vannucci L, Tort-colet N, Conti E, Resta F, Spalletti C, Ramalingasetty ST, von Arnim A, Formento E, Angelidis E, Blixhavn CH, Leergaard TB, Caleo M, Destexhe A, Ijspeert A, Micera S, Laschi C, Jirsa V, Gewaltig M, Pavone FS. Experimental and computational study on motor control and recovery after stroke: towards a constructive loop between experimental and virtual embodied neuroscience.. [DOI: 10.1101/2020.04.22.019661] [Reference Citation Analysis]
45 Yates SC, Groeneboom NE, Coello C, Lichtenthaler SF, Kuhn PH, Demuth HU, Hartlage-Rübsamen M, Roßner S, Leergaard T, Kreshuk A, Puchades MA, Bjaalie JG. QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front Neuroinform 2019;13:75. [PMID: 31849633 DOI: 10.3389/fninf.2019.00075] [Cited by in Crossref: 16] [Cited by in F6Publishing: 18] [Article Influence: 4.0] [Reference Citation Analysis]
46 Osen KK, Imad J, Wennberg AE, Papp EA, Leergaard TB. Waxholm Space atlas of the rat brain auditory system: Three-dimensional delineations based on structural and diffusion tensor magnetic resonance imaging. NeuroImage 2019;199:38-56. [DOI: 10.1016/j.neuroimage.2019.05.016] [Cited by in Crossref: 9] [Cited by in F6Publishing: 10] [Article Influence: 2.3] [Reference Citation Analysis]
47 Saleeba C, Dempsey B, Le S, Goodchild A, McMullan S. A Student's Guide to Neural Circuit Tracing. Front Neurosci 2019;13:897. [PMID: 31507369 DOI: 10.3389/fnins.2019.00897] [Cited by in Crossref: 64] [Cited by in F6Publishing: 69] [Article Influence: 16.0] [Reference Citation Analysis]