Minoru Koyama
Assistant Professor
Campus
UTSC
CSB Appointment
Full
Research Areas
Animal Biology, Biotechnology, Developmental Biology, Neurobiology, Physiology
Education
Ph.D. University of Tokyo 2006
M.Sc. University of Tokyo 2002
B.Sc. University of Tokyo 2000
Primary Undergraduate Department
Biological Sciences, UTSC
Graduate Programs
Cell & Systems Biology, Neuroscience
Research Description
I am interested in understanding the neural circuit mechanisms of behavioural development. Animals develop increasingly sophisticated behaviours after birth. Addressing the underlying mechanisms of circuit maturation in the brain is fundamental to understanding how neural circuits develop, are functionally organized, and operate. In addition, insights gained will provide a platform to aid our understanding of developmental brain disorders. We use zebrafish, an optically and genetically accessible model vertebrate that enables us to examine how circuit elements emerge, form circuitry, and contribute to behaviour across development through powerful combinations of optics, physiology, genetics and behavioural analyses.
My lab currently focuses on the circuit mechanisms of the development of sophisticated motor coordination. We are examining the circuit maturation in the hindbrain and the spinal cord that control the executive element of motor behaviours, using cutting-edge techniques such as two-photon optogenetics circuit mapping, voltage imaging, CRISPR/Cas9-based cell-type targeting and lineage tracing, photo-inducible cell ablation, and machine-learning-based behavioural analyses.
We are currently recruiting graduate students and postdoctoral fellows. Please inquire via email.
Contact Information
Office Phone: +1 416-208-8182
Office: SW525
Email
Mailing Address
Department of Cell & Systems Biology
University of Toronto
1265 Military Trail
Scarborough, ON M1C 1A4
Canada
Publications
2023
Multiplane HiLo microscopy with speckle illumination and non-local means denoising
Zheng S, Koyama M, Mertz J
2023, Journal of Biomedical Optics, 10.1117/1.JBO.28.11.116502
Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator
Abdelfattah AS, Zheng J, Singh A, Huang Y, Reep D, Tsegaye G, Tsang A, Arthur BJ, Rehorova M, Olson CV, Shuai Y, Zhang L, Fu T, Milkie DE, Moya MV, Weber TD, Lemire AL, Baker CA, Falco N, Zheng Q, Grimm JB, Yip MC, Walpita D, Chase M, Campagnola L, Murphy GJ, Wong AM, Forest CR, Mertz J, Economo MN, Turner GC, Koyama M, Lin B, Betzig E, Novak O, Lavis LD, Svoboda K, Korff W, Chen T, Schreiter ER, Hasseman JP, Kolb I
2023, Neuron, 10.1016/j.neuron.2023.03.009
High-resolution multi-z confocal microscopy with a diffractive optical element
Zhao B, Koyama M, Mertz J
2023, Biomedical Optics Express, 10.1364/BOE.491538
2022
TEMPO enables sequential genetic labeling and manipulation of vertebrate cell lineages
Espinosa-Medina I, Feliciano D, Belmonte-Mateos C, Linda Miyares R, Garcia-Marques J, Foster B, Lindo S, Pujades C, Koyama M, Lee T
2022, Neuron, 10.1016/j.neuron.2022.10.035
2021
In vivo glucose imaging in multiple model organisms with an engineered single-wavelength sensor
Keller JP, Marvin JS, Lacin H, Lemon WC, Shea J, Kim S, Lee RT, Koyama M, Keller PJ, Looger LL
2021, Cell Reports, 10.1016/j.celrep.2021.109284
Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator
Abdelfattah AS, Zheng J, Reep D, Tsegaye G, Tsang A, Arthur BJ, Rehorova M, Olson CV, Huang Y, Shuai Y, Koyama M, Moya MV, Weber TD, Lemire AL, Baker CA, Falco N, Zheng Q, Grimm JB, Yip MC, Walpita D, Forest CR, Chase M, Campagnola L, Murphy G, Wong AM, Mertz J, Economo MN, Turner G, Lin B, Chen T, Novak O, Lavis LD, Svoboda K, Korff W, Schreiter ER, Hasseman JP, Kolb I
2021, , 10.1101/2021.11.09.467909
TEMPO: A system to sequentially label and genetically manipulate vertebrate cell lineages
Espinosa-Medina I, Feliciano D, Belmonte-Mateos C, Garcia-Marques J, Foster B, Miyares RL, Pujades C, Koyama M, Lee T
2021, , 10.1101/2021.10.27.466134
2020
High-throughput cellular-resolution synaptic connectivity mapping in vivo with concurrent two-photon optogenetics and volumetric Ca2+ imaging
McRaven C, Tanese D, Zhang L, Yang C, Ahrens MB, Emiliani V, Koyama M
2020, , 10.1101/2020.02.21.959650
A fast genetically encoded fluorescent sensor for faithful in vivo acetylcholine detection in mice, fish, worms and flies
Borden PM, Zhang P, Shivange AV, Marvin JS, Cichon J, Dan C, Podgorski K, Figueiredo A, Novak O, Tanimoto M, Shigetomi E, Lobas MA, Kim H, Zhu PK, Zhang Y, Zheng WS, Fan C, Wang G, Xiang B, Gan L, Zhang G, Guo K, Lin L, Cai Y, Yee AG, Aggarwal A, Ford CP, Rees DC, Dietrich D, Khakh BS, Dittman JS, Gan W, Koyama M, Jayaraman V, Cheer JF, Lester HA, Zhu JJ, Looger LL
2020, , 10.1101/2020.02.07.939504
A programmable sequence of reporters for lineage analysis
Garcia-Marques J, Espinosa-Medina I, Ku K, Yang C, Koyama M, Yu H, Lee T
2020, Nature Neuroscience, 10.1038/s41593-020-0676-9
A general approach to engineer positive-going eFRET voltage indicators
Abdelfattah AS, Valenti R, Zheng J, Wong A, Podgorski K, Koyama M, Kim DS, Schreiter ER
2020, Nature Communications, 10.1038/s41467-020-17322-1
2019
In vivo glucose imaging in multiple model organisms with an engineered single-wavelength sensor
Keller JP, Marvin JS, Lacin H, Lemon WC, Shea J, Kim S, Lee RT, Koyama M, Keller PJ, Looger LL
2019, , 10.1101/571422
CLADES: a programmable sequence of reporters for lineage analysis
Garcia-Marques J, Yang C, Espinosa-Medina I, Koyama M, Lee T
2019, , 10.1101/655308
A general approach to engineer positive-going eFRET voltage indicators
Abdelfattah AS, Valenti R, Wong A, Koyama M, Kim DS, Schreiter ER
2019, , 10.1101/690925
Chronology-based architecture of descending circuits that underlie the development of locomotor repertoire after birth
Pujala A, Koyama M
2019, eLife, 10.7554/elife.42135
Dynamic super-resolution structured illumination imaging in the living brain
Turcotte R, Liang Y, Tanimoto M, Zhang Q, Li Z, Koyama M, Betzig E, Ji N
2019, Proceedings of the National Academy of Sciences, 10.1073/pnas.1819965116
Unlimited Genetic Switches for Cell-Type-Specific Manipulation
Garcia-Marques J, Yang C, Espinosa-Medina I, Mok K, Koyama M, Lee T
2019, Neuron, 10.1016/j.neuron.2019.07.005
Bright and photostable chemigenetic indicators for extended in vivo voltage imaging
Abdelfattah AS, Kawashima T, Singh A, Novak O, Liu H, Shuai Y, Huang Y, Campagnola L, Seeman SC, Yu J, Zheng J, Grimm JB, Patel R, Friedrich J, Mensh BD, Paninski L, Macklin JJ, Murphy GJ, Podgorski K, Lin B, Chen T, Turner GC, Liu Z, Koyama M, Svoboda K, Ahrens MB, Lavis LD, Schreiter ER
2019, Science, 10.1126/science.aav6416
2018
Unlimited genetic switches for cell-type specific manipulation
Garcia-Marques J, Yang C, Espinosa-Medina I, Mok K, Koyama M, Lee T
2018, , 10.1101/470443
Chronology-based architecture of descending circuits that underlie the development of locomotor repertoire after birth
Pujala A, Koyama M
2018, , 10.1101/425587
Bright and photostable chemigenetic indicators for extended in vivo voltage imaging
Abdelfattah AS, Kawashima T, Singh A, Novak O, Liu H, Shuai Y, Huang Y, Grimm JB, Patel R, Friedrich J, Mensh BD, Paninski L, Macklin JJ, Podgorski K, Lin B, Chen T, Turner GC, Liu Z, Koyama M, Svoboda K, Ahrens MB, Lavis LD, Schreiter ER
2018, , 10.1101/436840
Mutual inhibition of lateral inhibition: a network motif for an elementary computation in the brain
Koyama M, Pujala A
2018, Current Opinion in Neurobiology, 10.1016/j.conb.2017.12.019
50 Hz volumetric functional imaging with continuously adjustable depth of focus
Lu R, Tanimoto M, Koyama M, Ji N
2018, Biomedical Optics Express, 10.1364/boe.9.001964
Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms
Liu T, Upadhyayula S, Milkie DE, Singh V, Wang K, Swinburne IA, Mosaliganti KR, Collins ZM, Hiscock TW, Shea J, Kohrman AQ, Medwig TN, Dambournet D, Forster R, Cunniff B, Ruan Y, Yashiro H, Scholpp S, Meyerowitz EM, Hockemeyer D, Drubin DG, Martin BL, Matus DQ, Koyama M, Megason SG, Kirchhausen T, Betzig E
2018, Science, 10.1126/science.aaq1392
Brain-wide circuit interrogation at the cellular level guided by online analysis of neuronal function
Vladimirov N, Wang C, Höckendorf B, Pujala A, Tanimoto M, Mu Y, Yang C, Wittenbach JD, Freeman J, Preibisch S, Koyama M, Keller PJ, Ahrens MB
2018, Nature Methods, 10.1038/s41592-018-0221-x
A genetically encoded Ca2+ indicator based on circularly permutated sea anemone red fluorescent protein eqFP578
Shen Y, Dana H, Abdelfattah AS, Patel R, Shea J, Molina RS, Rawal B, Rancic V, Chang Y, Wu L, Chen Y, Qian Y, Wiens MD, Hambleton N, Ballanyi K, Hughes TE, Drobizhev M, Kim DS, Koyama M, Schreiter ER, Campbell RE
2018, BMC Biology, 10.1186/s12915-018-0480-0
2017
Video-rate volumetric functional imaging of the brain at synaptic resolution
Lu R, Sun W, Liang Y, Kerlin A, Bierfeld J, Seelig JD, Wilson DE, Scholl B, Mohar B, Tanimoto M, Koyama M, Fitzpatrick D, Orger MB, Ji N
2017, Nature Neuroscience, 10.1038/nn.4516
Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling
Liu H, Dong P, Ioannou MS, Li L, Shea J, Pasolli HA, Grimm JB, Rivlin PK, Lavis LD, Koyama M, Liu Z
2017, Proceedings of the National Academy of Sciences, 10.1073/pnas.1713895115
2016
A circuit motif in the zebrafish hindbrain for a two alternative behavioral choice to turn left or right
Koyama M, Minale F, Shum J, Nishimura N, Schaffer CB, Fetcho JR
2016, eLife, 10.7554/elife.16808
2011
Mapping a sensory-motor network onto a structural and functional ground plan in the hindbrain
Koyama M, Kinkhabwala A, Satou C, Higashijima S, Fetcho J
2011, Proceedings of the National Academy of Sciences, 10.1073/pnas.1012189108
A structural and functional ground plan for neurons in the hindbrain of zebrafish
Kinkhabwala A, Riley M, Koyama M, Monen J, Satou C, Kimura Y, Higashijima S, Fetcho J
2011, Proceedings of the National Academy of Sciences, 10.1073/pnas.1012185108
2006
MRI-based localization of electrophysiological recording sites within the cerebral cortex at single-voxel accuracy
Matsui T, Koyano KW, Koyama M, Nakahara K, Takeda M, Ohashi Y, Naya Y, Miyashita Y
2006, Nature Methods, 10.1038/nmeth987