Connectivity and Data Augmentation

Scholar Metrics Scraper (SMS), a novel tool that uses the scholarly package to automate data extraction from GS for groups of researchers.  Cao Y, Cheung NA, Giustini D, LeDue J and Murphy TH (2024) Scholar Metrics Scraper (SMS): automated retrieval of citation and author data. Front. Res. Metr. Anal. 9:1335454. doi: 10.3389/frma.2024.1335454

Scholar Metrics Scraper workflow diagram including the architecture and major steps.

A Raspberry Pi-based widefield imaging system to be used for close-proximity dual-brain cortical mesoscale functional-imaging to simultaneously observe activity in two head-fixed animals in a staged social touch-like interaction. Michelson, N. J., Bolaños, F., Bolaños, L. A., Balbi, M., LeDue, J. M., & Murphy, T. H. (2023). Meso-Py: Dual Brain Cortical Calcium Imaging in Mice during Head-Fixed Social Stimulus PresentationeNeuro10(12), ENEURO.0096-23.2023.

Yuhao YanTimothy H Murphy 2023 Decoding State-Dependent Cortical-Cerebellar Cellular Functional Connectivity in the Mouse Brain

Dongsheng XiaoYuhao YanTimothy H Murphy 2023 Mesotrode: chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice

Tony FongHao HuPankaj GuptaBraeden Jury and Timothy H. Murphy 2023 “PyMouseTracks: flexible computer vision and RFID based system for multiple mouse tracking and behavioral assessment” 

Ramandi D, Michelson NJ, Raymond LA, and Murphy TH 2023 Chronic multiscale resolution of mouse brain networks using combined mesoscale cortical imaging and subcortical fiber photometry in press Neurophotonics

Mesoscale cortex-wide neural dynamics predict goal-directed, but not random actions in mice several seconds prior to movement.  Mitelut C, Zhang Y, Sekino Y, Boyd JD, Bollanos F, Swindale NV, Silasi G, Saxena S, Murphy TH Elife in press

Multiscale imaging informs translational mouse modeling of neurological disease.  Wang Y, LeDue JM, and Murphy TH 2022 DOI: Neuron

Hu H, Xiao D, Rhodin H, Murphy TH. Towards a Visualizable, De-identified Synthetic Biomarker of Human Movement Disorders.  J Parkinsons Dis. 1(-1):2085-2096. doi: 10.3233/JPD-223351. (2022) PMID: 36057831

Bolaños LA, Xiao D, Ford NL, LeDue JM, Gupta PK, Doebeli C, Hu H, Rhodin H, and Murphy TH   A 3D virtual mouse generates synthetic training data for behavioral analysis.  Nature Methods volume 18, pages 378–381(2021)


Murphy TH, Boyd JD, Michelson N, Fong T, Bolaños LA, Bierbrauer D, Siu T, Gupta PK, Balbi M, Bolaños F, Vanni M, and LeDue JM (2020) Automated task training and longitudinal monitoring of mouse mesoscale cortical circuits using homecages. eLife 2020 May 15;9:e55964.doi: 10.7554/eLife.55964.


Task dependent cortical activity being collected 24/7, each image is a bi-hemispheric mouse cortex.


McGirr A, LeDue J, Chan AW, Boyd JD, Metzak PD, Murphy TH (2020) Stress impacts sensory variability through cortical sensory activity motifs. Transl Psychiatry. 2020 Jan 21;10(1):20. doi: 10.1038/s41398-020-0713-1.

Woodard C, Nasrallah W, Samiei B, Murphy TH, and Raymond LA. (2020) PiDose: An open-source system for accurate and automated oral drug administration to group-housed mice. Sci Rep. 2020 Jul 14;10(1):11584. doi: 10.1038/s41598-020-68477-2.

Forys B, Xiao D, Gupta PK, Boyd JD, Murphy TH (2020) Real-time markerless video tracking of forepaw in head-fixed mice using deep neural networks. eNeuro 2020 Jun 15;7(3):ENEURO.0096-20.2020. doi: 10.1523/ENEURO.0096-20.2020.

Mitelut C., Spacek M., Chan A., Murphy T., Swindale N. (2019) LFP clustering in cortex reveals a taxonomy of UP-states and near-millisecond, ordered phase-locking in cortical neurons. J Neurophysiol. 2019 Oct 1;122(4):1794-1809. doi: 10.1152/jn.00456.2019. Epub 2019 Aug 21.

Ashby D., LeDue J. , Murphy T. , McGirr A. (2019) Peripheral nerve ligation elicits widespread alterations in cortical sensory evoked and spontaneous Activity. Sci Rep. 2019 Oct 25;9(1):15341. doi: 10.1038/s41598-019-51811-8.

Gupta PK, Murphy TH. (2019) Cortex-wide Computations in Complex Decision Making in Mice. Neuron. 2019 Nov 20;104(4):631-633. doi: 10.1016/j.neuron.2019.10.043.

Michelson NJ, Vanni MP, Murphy TH. (2019) Comparison between transgenic and AAV-PHP.eB-mediated expression of GCaMP6s using in vivo wide-field functional imaging of brain activity. Neurophotonics. 2019 Apr;6(2):025014. doi: 10.1117/1.NPh.6.2.025014. Epub 2019 Jun 22.

Chan, A.W. & Murphy, T.H. (2017) Good Vibrations: Resting-State Functional Connectivity Reflects Entrainment of Vasomotion. Neuron, 96, 716-717.

Silasi, G., Boyd, J.D., Bolanos, F., LeDue, J.M., Scott, S.H. & Murphy, T.H. (2018) Individualized tracking of self-directed motor learning in group-housed mice performing a skilled lever positioning task in the home cage. J Neurophysiol, 119, 337-346.

Woodard, C.L., Bolanos, F., Boyd, J.D., Silasi, G., Murphy, T.H. & Raymond, L.A. (2017) An Automated Home-Cage System to Assess Learning and Performance of a Skilled Motor Task in a Mouse Model of Huntington’s Disease. eNeuro, 4.

Vanni, M.P., Chan, A.W., Balbi, M., Silasi, G. & Murphy, T.H. (2017) Mesoscale Mapping of Mouse Cortex Reveals Frequency-Dependent Cycling between Distinct Macroscale Functional ModulesJ Neurosci, 37, 7513-7533.

Noorshams, O., Boyd, J.D. & Murphy, T.H. (2017) Automating mouse weighing in group homecages with Raspberry Pi micro-computers. J Neurosci Methods, 285, 1-5.

Haupt, D., Vanni, M.P., Bolanos, F., Mitelut, C., LeDue, J.M. & Murphy, T.H. (2017) Mesoscale brain explorer, a flexible python-based image analysis and visualization tool. Neurophotonics, 4, 031210.

Xiao D., Vanni MP., Mitelut C., Chan AW., Xie Y., Chen AC., Swindale, NV., and Murphy TH. (2017) Mapping cortical mesoscopic networks of single spiking cortical or sub-cortical neurons. eLife e19976. doi: 10.7554/eLife.19976

McVea DA, Murphy TH, Mohajerani MH. (2016) Large Scale Cortical Functional Networks Associated with Slow-Wave and Spindle-Burst-Related Spontaneous Activity. Front Neural Circuits. doi: 10.3389/fncir.2016.00103. Review.

Bolanos, F. and LeDue J., Murphy TH. (2017) Cost effective raspberry pi-based radio frequency identification tagging of mice suitable for automated in vivo imaging. J. Neurosci. Meth. 276:79-83.

Murphy TH, Boyd JD, Bolaños F, Vanni MF, Silasi G, Haupt D,  LeDue JM. (2016) High-throughput automated home-cage mesoscopic functional imaging of mouse cortex. Nature Communications 7:11611.

Silasi G, Xiao D, Vanni MP, Chen AC, Murphy TH (2016) Intact skull chronic windows for mesoscopic wide-field imaging in awake mice. (2016) J Neurosci Methods. 15:141-9.

Xie Y, Chan AW, McGirr A, Xue S, Xiao D, Zeng H, Murphy TH (2016) Resolution of High-Frequency Mesoscale Intracortical Maps Using the Genetically Encoded Glutamate Sensor iGluSnFR. J Neurosci 36:1261-1272.

Zeng S, Murphy TH (2015) Special Section Guest Editorial: Special Section on Light Microscopy of Connectivity. Neurophotonics 2:041401.

Funayama K, Minamisawa G, Matsumoto N, Ban H, Chan AW, Matsuki N, Murphy TH, Ikegaya Y (2015) Neocortical Rebound Depolarization Enhances Visual Perception. PLoS Biol 13:e1002231.

Lacroix A, Toussay X, Anenberg E, Lecrux C, Ferreiros N, Karagiannis A, Plaisier F, Chausson P, Jarlier F, Burgess SA, Hillman EM, Tegeder I, Murphy TH, Hamel E, Cauli B (2015) COX-2-Derived Prostaglandin E2 Produced by Pyramidal Neurons Contributes to Neurovascular Coupling in the Rodent Cerebral Cortex. J Neurosci 35:11791-11810.

Chan AW, Mohajerani MH, LeDue JM, Wang YT, Murphy TH (2015) Mesoscale infraslow spontaneous membrane potential fluctuations recapitulate high-frequency activity cortical motifs. Nat Commun 6:7738.f

Anenberg E, Chan AW, Xie Y, LeDue JM, Murphy TH (2015) Optogenetic stimulation of GABA neurons can decrease local neuronal activity while increasing cortical blood flow. J Cereb Blood Flow Metab. 35:1579-1586.

Lim DH, LeDue JM, Murphy TH (2015) Network analysis of mesoscale optical recordings to assess regional, functional connectivity. Neurophotonics 2:041405.

Vanni, M. and Murphy T.H. (2014) Mesoscale transcranial spontaneous activity mapping in GCaMP3 transgenic mice reveals extensive reciprocal connections between areas of somatomotor cortex. J. of Neurosci. 34(48):15931-46.

Harrison, T.C., and Murphy, T.H. (2014). Motor maps and the cortical control of movement. Curr Opin Neurobiol 24: 88-94.

Mohajerani MH, Chan AW, Mohsenvand M, Ledue J, Liu R, McVea DA, Boyd JD, Wang YT, Reimers M, Murphy TH. (2013) Spontaneous cortical activity alternates between motifs defined by regional axonal projections. Nat Neurosci. 2013 16:1426-35.

Silasi G., Boyd, J.D., LeDue J. and Murphy TH. (2013) Improved methods for chronic light-based motor mapping in mice: automated movement tracking with accelerometers, and chronic EEG recording in a bilateral thin-skull preparation. Front Neural Circuits. 7:123.

Lim DH, Ledue J, Mohajerani MH, Vanni MP, Murphy TH. (2013) Optogenetic approaches for functional mouse brain mapping. Front Neurosci. 7:54. doi: 10.3389/fnins.2013.00054.

Harrison TC, Murphy TH. (2012) Towards a circuit mechanism for movement tuning in motor cortex. Front Neural Circuits. 6:127. doi: 10.3389/fncir.2012.00127. Epub 2013 Jan 18.

Harrison TC, Ayling OG, Murphy TH. (2012) Distinct Cortical Circuit Mechanisms for Complex Forelimb Movement and Motor Map Topography. Neuron. 74:397-409. doi: 10.1016/j.neuron.2012.02.028.

Lim, D.H. M.H. Mohajerani, Boyd J., LeDue J., Chen S., and Murphy T.H. (2012) In vivo large-scale cortical mapping using channelrhodopsin-2 stimulation in transgenic mice reveals asymmetric and reciprocal relationships between cortical areas. Front. Neural Circuits 6:11. doi: 10.3389/fncir.2012.00011.

Scott N.A., Murphy T.H & Illes J. (2012) Incidental findings in neuroimaging research: a framework for anticipating the next frontier. Journal of Empirical Research on Human Research Ethics, DOI: 10.1525/jer.2012.7.1.53.

Scott, N., Murphy, T.H. (2012) Hemodynamic responses evoked by selective neuronal stimulation via channelrhodopsin-2 are independent of intracortical ionotropic excitatory synaptic transmission. PLoS ONE 7(1): e29859. doi:10.1371.

Arstikaitis P, Gauthier-Campbell C, Huang K, El-Husseini A, Murphy TH (2011) Proteins that promote filopodia stability, but not number, lead to more axonal-dendritic contacts. PLoS One 6:e16998.

Takahashi H, Arstikaitis P, Prasad T, Bartlett TE, Wang YT, Murphy TH, Craig AM (2011) Postsynaptic TrkC and presynaptic PTPsigma function as a bidirectional excitatory synaptic organizing complex. Neuron 69:287-303.

Scott NA, Murphy TH (2011) Glial laminar cortical architecture matches metabolic demand. J Cereb Blood Flow Metab 31:793-794.

Mohajerani MH, McVea DA, Fingas M, and Murphy TH (2010) Mirrored bilateral slow-wave cortical activity within local circuits revealed by fast bihemispheric voltage-sensitive dye imaging in anesthetized and awake mice. J Neurosci 30:3745-51.

Harrison TC, Sigler A, and Murphy TH. (2009) Simple and cost-effective hardware and software for functional brain mapping using Intrinsic Optical Signal imaging. J Neurosci Methods 182:211-218.

Ayling OG, Harrison TC, Boyd JD, Goroshkov A, and Murphy TH. (2009) Automated light-based mapping of motor cortex by photoactivation of channelrhodopsin-2 transgenic mice. Nat Methods 6:219-224.
*Supported in part by the Estate of Erika W. White. The purpose of this fund is to support research into the medical use of laser technology.

Gauthier-Campbell C, Carolina Gutierrez-Herrera R, Huang K, Levinson JN, Murphy TH, Kilimann MW, Sala C, Colicos MA, and El-Husseini A (2008) Paralemmin-1, a Modulator of filopodia induction is required for spine maturation. Mol Biol Cell 19:2026-2038.

Liu Z, Otsu Y, Vasuta C, Nawa H, and Murphy TH (2007) Action-potential-independent GABAergic tone mediated by nicotinic stimulation of immature striatal miniature synaptic transmission. J Neurophysiol 98:581-593.

Winship IR, Plaa N, and Murphy TH (2007) Rapid astrocyte calcium signals correlate with neuronal activity and onset of the hemodynamic response in vivo. J Neurosci 27:6268-6272.

Awatramani GB, Boyd JD, and Delaney KR, Murphy TH (2007) Effective release rates at single rat Schaffer collateral-CA1 synapses during sustained theta-burst activity revealed by optical imaging. J Physiol 582:583-595.

Liu Z, Ren J, and Murphy TH (2003) Decoding of synaptic voltage waveforms by specific classes high threshold calcium channels. J Physiol 553:473-488

Otsu Y and Murphy TH (2003) Mind-altering miniature neurotransmitter release? Proc Natl Acad Sci U S A. 100:5589-90.

Prange O and Murphy TH (2001) Modular Transport of Postsynaptic Density-95 Clusters and Association with Stable Spine Precursors during Early Development of Cortical Neurons. J Neurosci 21:9325-9333.

Mackenzie PJ, Kenner GS, Prange O, and Murphy TH (2000) Vesicle number does not predict postsynaptic measures of miniature synaptic activity frequency in cultured cortical neurons. Neuroscience 98:1-7. See our cover photo above. 

Umemiya M, Senda M, and Murphy TH (1999) Behavior of NMDA and AMPA receptor mediated miniature excitatory synaptic currents at synapses identified by calcium imaging. J Physiol (Lond). 521:113-22.

Nakazawa H and Murphy TH. (1999) Activation of nuclear calcium dynamics by synaptic stimulation in cultured cortical neurons. J Neurochem 73:1075-1083.

Mackenzie PJ, Kenner GS, Prange O, Shayan H, Umemiya M, and Murphy TH (1999) Ultrastructural correlates of quantal synaptic function at single CNS synapses. J Neurosci 19:RC13.

Wang S, Prange O, and Murphy TH (1999) Amplification of calcium signals at dendritic spines provides a method for CNS quantal analysis. Canadian J of Physiol Pharmacol 77:651-659.

Mackenzie PJ, Umemiya M, and Murphy TH (1996) Ca2+ imaging of CNS axons in culture indicates reliable coupling between single action potentials and distal functional release sites. Neuron 16:783-795. See our cover photo above. 

Murphy TH, Baraban JM, and Wier WG (1995) Mapping miniature synaptic currents to single synapses using calcium imaging reveals heterogeneity in postsynaptic output. Neuron 15:159-168.

Murphy TH, Baraban JM, Wier WG, and Blatter LA (1994) Visualization of quantal synaptic transmission by dendritic calcium imaging. Science 263:529-532.

Murphy TH, Blatter LA, Wier WG, and Baraban JM (1993) Rapid communication between neurons and astrocytes in primary cortical cultures. J Neurosci 13:2672-2679.

Murphy TH, Worley PF, and Baraban JM (1991) L-type voltage-sensitive calcium channels mediate synaptic activation of immediate early genes. Neuron 7:625-635.