Stepwise optogenetic activation of the rat thalamic nuclei with MRI-guided robotic arm (MgRA)
Yi Chen1,2, Patricia Pais-Roldán1,2, Xuming Chen1, and Xin Yu1

1Research Group of Translational Neuroimaging and Neural Control, High-Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tuebingen, Germany, 2Graduate School of Neural Information Processing, University of Tuebingen, Tuebingen, Germany


An MRI-guided multiple degree-of-freedom robotic arm positioning system is developed to guide the fiber optic insertion inside a small animal MRI scanner. The fiber optic is positioned at different depth in the rat thalamus to deliver light pulses for optogenetic fMRI. The corresponding functional spatial patterns and time courses can be achieved in a stepwise manner. The MgRA positioning system provides an alternative way to study global functional projections by mapping fMRI signals driven optogenetically from different brain nuclei.

Target Audience

Scientists who are interested in high resolution fMRI, cerebrovascular imaging and optogenetics.


Cortical states profoundly regulate many aspects of behavior, from states of consciousness to perception, learning and cognition1. The thalamus contains ~40 nuclei, each innervating a different combination of cortical areas2. It remains challenging to characterize the precise functional projections of individual thalamic subdivisions to the cortex despite the existing resting-state functional connectivity mapping schemes3. Optogenetic fMRI allows visualization of the causal effects of specific neural projection circuits defined not only by genetic identity and cell body location, but also by axonal projection target4. Therefore, an MRI-guided robotic arm (MgRA) positioning system with high targeting accuracy and precision is crucial to target optic fiber at different thalamic nuclei and map the BOLD-fMRI functional patterns globally.


An MRI-compatible MgRA positioning system was developed for the 14.1T horizontal MR scanner with 12cm inner diameter gradient (Fig.1a). Fig.1c illustrates the camera-based visual guidance of fiber optic positioning on the rat skull craniotomy at the iso-center of the horizontal bore magnet. Driven by MgRA, the optic fiber was inserted to target multiple coordinates in the thalamus. A 24mm-diameter custom-designed transmit/receive surface coil was attached on the rat head. Anatomical images for fiber location were acquired using 2D rapid acquisition with relaxation enhancement sequence: TR, 1200ms, TE, 7ms, 1.92cmX1.50cm FOV, 128X100 matrix, 150X150um in-plane resolution, 800um thickness. fMRI scans were performed using 3D Echo planar imaging sequence: TR, 1.5s, TE,11.5ms, 1.92X1.92X1.92cm3 FOV, 48X48X48 matrix, 400X400X400 um3 spatial resolution. Fig.1b demonstrates three continuous MRI images with step distance 400um. AAV5.CAG.ChR2.mcherry viral vectors were stereotaxically injected in the thalamus in 4-week old rats. The detailed surgical procedures for optogenetic fMRI were described previously5. The optical fiber(~200um) delivered blue light pulses (473nm) at 5Hz, 10ms width with 4s duration for the fMRI block design. The EPI-fMRI data were acquired in a stepwise manner when the fiber optic was inserted at different locations of the thalamus. MRI data analysis was performed using Analysis of Functional NeuroImages software(NIH, Bethesda).


Fig 2 shows the broad cortical activation after the optogenetic stimulation of the thalamus. Although the fiber optic was located at the dorsal part of the thalamus, the BOLD signal spread through the major cortical regions in the ipsilateral hemisphere, as well as a small part of the contralateral hemisphere. In addition, the BOLD signal could be detected at the thalamic regions close to the fiber tip. Fig 3 shows the BOLD signal changes of the somatosensory cortex when the fiber optic was lowered at different depth of the thalamus. It clearly showed that the amplitude of the BOLD signal approached to peak when the fiber optic was at the depth (trial # 37) and gradually decreased when the fiber was inserted to deeper thalamic area ( trial # 55).


The optogenetically stepwise activation of different thalamic nuclei can be achieved by the MgRA positioning system. This work shows that MgRA provides a precise and effective method to target multiple deep brain nuclei and makes it possible to map the functional activation patterns consecutively along the fiber insertion trajectory.


We thank Mr. Shanyi Yu for building up the first prototype of the robotic arm and Mr. Johannes Boldt for helping to improve the MgRA system. The financial support of the Max-Planck-Society and the China Scholarship Council (PhD fellowship to Yi Chen) are gratefully acknowledged.


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2. Jones, E.G. The Thalamus, 2 Volume Set (Cambridge University Press, 2007).

3. Monica Giraldo-Chica, Neil D. Woodward. Review of thalamocortical resting-state fMRI studies in schizophrenia. Schizophrenia Research. (2016),http://dx.doi.org/10.1016/j.schres.2016.08.005

4. Lee JH, Durand R, et al. Global and local fMRI signals driven by neurons defined optogenetically by type and wiring. Nature; 2010:465(7299):788-792.

5. Yu X, He Y, Wang M, Merkle H, Dodd SJ, Silva AC and Koretsky AP. Sensory and optogenetically driven single-vessel fMRI. Nature Methods;13:337-340.


Fig. 1. Optogenetically driven fMRI with MgRA experiment procedure. a. Robotic arm setup in the 14.1T scanner. b. The time-lapsed images to show fiber optic targeting different depth in the rat thalamus. c. Camera monitored fiber position above the hole on the rat skull. d. Thalamic injection of AAV5.CAG.ChR2.mcherry and optical stimulation.

Fig. 2. a. Fiber location in the rat brain. b. The global activation pattern upon optogenetic photo-activation of the thalamus. c. The light-driven fMRI signal time course from the activated ipsilateral voxeI. d. The time course of the BOLD signal from cortical (red) and thalamus (blue) ROIs.

Fig. 3. a. Depth of fiber based BOLD signal changes. b. Location of the fiber in the rat Thalamus.

Proc. Intl. Soc. Mag. Reson. Med. 25 (2017)