OptofMRI5HT [Hamada et al., Nat Commu, 2024]

This is the code repository for the project about optogenetic fMRI stimulating dorsal raphe serotonin neurons [Hamada et al., Nat Commu, 2024]. The dataset is also available from Openneuro (project ID: optofMRI_DRN)

Findings of the works

1. Functional map of serotonergic activation by optogenetics, including reward-related network
2. General anesthetics, isoflurane, reverses brain-wide activation by DRN stimulation
3. Functional map was correlated with structural density.
4. The expression of 5-HT receptors and structural density can explain the functional maps.
5. General anesthetics may change receptor response.

Experiments

The experiment is composed of four sessions.

• Session 1. in awake state
• Session 2. in awake state (replication)
• Session 3. in anesthesia
• Session 4. in awake state

Data

• 1. Time Series of each session
• 2. beta values of each session
• 3. ROIs: 28 Regions of Interest (ROIs)

(Raw data will be available from Openneuro soon.)

Prerequisite

For this study, we introduced the following software tools.

Software List
ID	Name	Contributor	Purpose	URLs
1	Statistical Parametric Mapping 12(SPM12)	The Wellcome Centre for Human Neuroimaging, UCL	MRI data analysis	https://www.fil.ion.ucl.ac.uk/spm
2	MarsBaR region of interest toolbox for SPM		Brain Reference Registration	http://marsbar.sourceforge.net/
3	MRIcroGL	Chris Rorden, Neuropsychology Lab, University of South Carolina	3D visualization of MRI data	https://www.nitrc.org/projects/mricrogl/
4	Probabilistic Threshold-free Cluster Enhancement (pTFCE) [1]	Tamás Spisák	A cluster-enhancement method	https://spisakt.github.io/pTFCE/
5	Allen Brain Atlas	Allen Brain Institutes	Reference atlas, 5HT projection map, 5HT receptor gene expressions	https://portal.brain-map.org/
6	Templates for In Vivo Mouse Brain [2]	Keigo Hikishima (k-hikishima@ aist.go.jp)	Mouse brain templates for registration and normalization	https:// www.nitrc.org/ projects/tpm_mouse
7	Gramm [3]	Pierre Morel	Visualization of Plotting	https://github.com/piermorel/gramm
8	in-house analysis programs	Hiro Taiyo Hamada ([email protected])	Analysis for time series, Behavioral analysis	https://github.com/Taiyou/OptofMRI_5HT
9	MATLAB2020b	MathWorks	Main analyses and data visualization	https://mathworks.com/
10	A CBV opfMRI dataset	Joanes Grandjean	Analysis for functional maps	https://doi.org/10.18112/openneuro.ds001541.v1.1.2 https://doi.org/10.34973/raa0-5z29

Program

Please install and make a path to Gramm prior to running the codes.

% check if all codes are functional.
run_allcodes

1. Allen Brain Atlas

• AllenBrainAtlas/AllenAtlasNorm.r
• AllenBrainAtlas/TemplateNorm.r

2. Figure 2b, Figure 5a, Supplementary Figure S4

main_COPE_session1_TestandPlot

3. Figure 3c

main_COPE_session34_TestandPlot

4. Figure 3d & Supplementary Figure S11

visualizeAllTimeSeriesSession3vs4

5. Figure 4b-c, Figure 5b-d, Table 3 & Supplementary Table TS3

 main_corr5HTprojAndCOPE

6. Supplementary Figure S5 & S6

visualizeAllTimeSeriesSession1st

7. Supplementary Figure S7

supp_contrastBetweenSession1vs2

8. Supplementary Figure S8 a-b & S9

supp_consistencyBetweenSession1AndSession2

9. Supplementary Figure S8 c-d

supp_peaktimingANDBOLDconsistency

10. Supplementary Figure S14

suppS14_extraction_TSdata_madino

11. Supplementary Figure S15

• 5HTR_correlation_plot.ipynb

12. Appendix

% Motion Artefacts
cd motion_artefacts
run_session1MACheck
run_session2MACheck
run_session3MACheck
run_session4MACheck
run_comparison_ane1stVSane2nd

Reference

1. Spisák, T., Spisák, Z., Zunhammer, M., Bingel, U., Smith, S., Nichols, T., & Kincses, T. (2019). Probabilistic TFCE: A generalized combination of cluster size and voxel intensity to increase statistical power. NeuroImage, 185, 12–26. https://doi.org/10.1016/j.neuroimage.2018.09.078
2. Hikishima, K., Komaki, Y., Seki, F., Ohnishi, Y., Okano, H. J., & Okano, H. (2017). In vivo microscopic voxel-based morphometry with a brain template to characterize strain-specific structures in the mouse brain. Scientific reports, 7(1), 85. https://doi.org/10.1038/s41598-017-00148-1
3. Morel, (2018). Gramm: grammar of graphics plotting in Matlab. Journal of Open Source Software, 3(23), 568, https://doi.org/10.21105/joss.00568
4. Hamada H.T., Abe Y., Takata N., Taira M, Tanaka F.K., and Doya K. Optogenetic activation of dorsal raphe serotonin neurons induces brain-wide activation. Nat Commu, 15, 4152. https://doi.org/10.1038/s41467-024-48489-6 Preprint Dataset Codes