View on GitHub

Jumpei Matsumoto, Ph.D.

System Emotional Science, University of Toyama, Japan

Download this project as a .zip file Download this project as a tar.gz file


I am a Japanese neuroscientist working at System Emotional Science in University of Toyama. This page is for self-introduction and distribution of our software for research.

| News | 3DTracker | Publications | Forum |


(May/23/2017) We launched an web site for 3DTracker (, for futher sharing the work and open-source development. Check it and join us!

(Dec/14/2016) 3DTracker has been applied for monkey motion capture. link to the paper

(Dec/14/2016) 3DTracker has been used with electrophysiological recording and ultrasound recording for investigating naturalistic social behavior in rats link to the paper

(Jul/20/2014) 3DTracker was applied for analyzing object recognition test. link to the paper

(Jul/20/2014) Our software was reviewed by Dell et al. (2014) in Trends in Ecology and Evolution.


Check the for further information about the software.

screen shot
See also a video. 動画はこちら

We developed a novel 3D marker-less motion capture and behavior analysis system for interacting rodents, named 3DTracker. It’s open-source software available at PLoS ONE. We are going to provide updates of the software, documents, examples of applications, user communication forum and more, through a special web site,


Nakamura T, Matsumoto J, Nishimaru H, Bretas R, Takamura Y, Hori E, Ono T, Nishijo H. A markerless 3D computerized motion capture system incorporating a skeleton model for monkeys. PLoS One 2016 Nov 3;11(11):e0166154

Matsumoto J, Nishimaru H, Takamura Y, Urakawa S, Ono T, Nishijo H. Amygdalar auditory neurons contribute to self-other distinction during ultrasonic social vocalization in rats. Front Neurosci 10:399

Matsumoto J, Nishimaru H, Ono T, Nishijo H. 3D-video-based computerized behavioral analysis for in vivo neuropharmacology and neurophysiology in rodents. In: In Vivo Neuropharmacology and Neurophysiology (ed., Philippou A), Springer, NY, 2017, in press

de Araujo MF, Matsumoto J, Ono T, Nishijo H. An animal model of disengagement: Temporary inactivation of the superior colliculus impairs attention disengagement in rats. Behav Brain Res 2015 Oct 15;293:34-40

Fuzzo F, Matsumoto J, Kiyokawa Y, Takeuchi Y, Ono T, Nishijo H. Social buffering suppresses fear-associated activation of the lateral amygdala in male rats: behavioral and neurophysiological evidence. Front Neurosci 2015 Mar 25;9:99

Nakamura T, Matsumoto J, Takamura Y, Ishii Y, Sasahara M, Ono T, Nishijo H. Relationships among parvalbumin-immunoreactive neuron density, phase-locked gamma oscillations, and autistic/schizophrenic symptoms in PDGFR-β knock-out and control mice. PLoS One 2015 Mar 24;10(3):e0119258

Ngan NH, Matsumoto J, Takamura Y, Tran AH, Ono T, Nishijo H. Neuronal correlates of attention and its disengagement in the superior colliculus of rat. Front Integr Neurosci 2015 Feb 18;9:9. doi: 10.3389/fnint.2015.00009. eCollection 2015

Matsumoto J, Uehara T, Urakawa S, Takamura Y, Sumiyoshi T, Suzuki M, Ono T, Nishijo H. (2014) 3D video analysis of the novel object recognition test in rats. Behav Brain Res., pii: S0166-4328(14)00430-6

Enkhjargal N, Matsumoto J, Chinzorig C, Berthoz A, Ono, T, & Nishijo H. (2014) Rat thalamic neurons encode complex combinations of heading and movement directions and the trajectory route during translocation with sensory conflict. Front Behav Neurosci., 8:242.

Nguyen CL, Tran AH, Matsumoto J, Hori E, Uwano T, Ono T, Nishijo H. (2014) Hippocampal place cell responses to distal and proximal cue manipulations in dopamine D2 receptor-knockout mice. Brain Res., 3;1567:13-27

Nguyen MN, Matsumoto J, Hori E, Maior RS, Tomaz C, Tran AH, Ono T, Nishijo H. (2014) Neuronal responses to face-like and facial stimuli in the monkey superior colliculus. Front Behav Neurosci., 17;8:85

Nguyen HM, Matsumoto J, Tran AH, Ono T, Nishijo H. (2014) sLORETA current source density analysis of evoked potentials for spatial updating in a virtual navigation task. Front Behav Neurosci., 8:66

Zhao J, Urakawa S, Matsumoto J, Li R, Ishii Y, Sasahara M, Peng Y, Ono T, Nishijo H. (2013) Changes in Otx2 and Parvalbumin Immunoreactivity in the Superior Colliculus in the Platelet-Derived Growth Factor Receptor- β Knockout Mice. Biomed Res Int., 2013:848265

Hori S, Matsumoto J, Hori E, Kuwayama N, Ono T, Kuroda S, Nishijo H. (2013) Alpha- and theta-range cortical synchronization and corticomuscular coherence during joystick manipulation in a virtual navigation task. Brain Topogr, 26(4):591-605

Matsumoto J, Urakawa S, Takamura Y, Malcher-Lopes R, Hori E, Tomaz C, Ono T, and Nishijo H (2013) A 3D-video-based computerized analysis of social and sexual interactions in rats. PLoS ONE 8:e7846

Le Q, Isbell LA, Matsumoto J, Nguyen M, Hori E, Maior RS, Tomaz C, Tran AH, Ono T, Nishijo H (2013) Pulvinar neurons reveal neurobiological evidence of past selection for rapid detection of snakes. PNAS, 110(47):19000-5

Furuya Y, Matsumoto J, Hori E, Boas CV, Tran AH, Shimada Y, Ono T, Nishijo H (2013) Place-related neuronal activity in the monkey parahippocampal gyrus and hippocampal formation during virtual navigation. Hippocampus, 24(1):113-30

Takamura Y, Ono K, Matsumoto J, Yamada M, Nishijo H (2013) Effects of the neurotrophic agent T-817MA on oligomeric amyloid-β-induced deficits in long-term potentiation in the hippocampal CA1 subfield. Neurobiology of Aging, 35(3):532-6

Nguyen MN, Hori E, Matsumoto J, Tran AH, Ono T, Nishijo H. (2013) Neuronal responses to face-like stimuli in the monkey pulvinar. Eur J Neurosci. 37(1):35-51

Matsumoto J, Urakawa S, Hori E, Araujo M. F. P., Sakuma Y, Ono T, Nishijo H (2012) Neuronal responses in the nucleus accumbens shell during sexual behavior in male rats. Journal of Nuroscience 32:1672-1686

Aitake M, Hori E, Matsumoto J, Umeno K, Fukuda M, Ono T, Nishijo H Sensory mismatch induces autonomic responses associated with hippocampal theta waves in rats. Behavioural Brain Research, Vol. 220, pp 244-53, 2011

Matsumoto J, Makino Y, Miura H, Yano M (2011) A computational model of the hippocampus that represents environmental structure and goal location, and guides movement. Biological Cybernetics 105: 139-152