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In Vivo Diffusion MRI of Optic Pathways in 18 Healthy Mice

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This dataset contains manganese-enhanced T1-weighted and diffusion-weighted MRI of the optic pathways in 18 healthy C57BL/6 female mice.
The study investigates white matter organization and manganese transport in the mouse visual system using in vivo high-field MRI.
Raw Bruker files and a subset of NIfTI-converted images are included to support both reprocessing and immediate analysis.

License

Creative Commons Attribution 4.0 International (CC BY 4.0)

Citation

Filipiak, P., Sajitha, T. A., Shepherd, T. M., Clarke, K., Goldman, H., Placantonakis, D. G., Zhang, J., Chan, K. C., Boada, F. E., & Baete, S. H. (2023).
In vivo diffusion MRI of optic pathways in 18 healthy mice [Data set]. Zenodo.
https://doi.org/10.5281/zenodo.8120834

Source

https://doi.org/10.5281/zenodo.8120834
Institution: NYU Langone Health, Center for Advanced Imaging Innovation and Research (CAI2R)
Contact: steven.baete@nyulangone.org
Funded by: NIH grants R01 EB028774, R01 EB029306, R01 NS082436, P41 EB017183, and 1S10OD018337-01.

Dataset Information

Category Details
Species Mouse (Mus musculus, C57BL/6 females)
Sample Size n = 18
Age 7–8 weeks at imaging
Scanner 7 T Bruker BioSpec (wide-bore)
Coil 4-channel phased-array cryogenically cooled receive-only coil
Anesthesia Isoflurane (3% induction, 1.0–1.5% maintenance)
Imaging Sequences T1-weighted FLASH and multi-shell DWI
DWI Parameters 200 µm isotropic, TE/TR = 27.6/2781 ms, 60 directions, b = {250, 1000, 2250, 4000} s/mm²
T1-weighted Parameters FLASH, 100 µm isotropic, TE/TR = 4.5/30 ms
Acquisition Time ~37 min (effective 60–70 min with motion-triggering)
Data Format Bruker raw data and converted NIfTI files
Total Dataset Size ~26 GB

Experimental Protocol

Following baseline imaging, each mouse received intravitreally administered manganese chloride (MnCl₂) to enhance the T1-weighted signal along the visual pathways.

  • Injection volume: 1.0 µL (Mice 1–2), reduced to 0.5 µL (Mice 3–18) of 0.1 M MnCl₂
  • Injection side: Left eye (n = 8) or right eye (n = 10)
  • Follow-up scan: 21 ± 4 hours post-injection using the same FLASH T1-weighted sequence

To minimize motion artifacts, mice were secured using a bite bar and ear bars and monitored via a breathing pressure pad coupled to a TTL-triggered acquisition system.

Image Processing

The DWI preprocessing pipeline employed MRtrix3 and ANTs tools:

  • Denoising: dwidenoise (MP-PCA)
  • Gibbs artifact removal: mrdegibbs
  • Bias field correction: dwibiascorrect ants
  • Resampling: Interpolation to 100 µm isotropic resolution (matching anatomical scans)
  • Registration: antsRegistrationSyN.sh (rigid-body transform aligning follow-up MEMRI to b=0 images)

Acknowledgments

This work was supported by the NIH Center for Advanced Imaging Innovation and Research (CAI2R), a NIBIB Biomedical Technology Resource Center (P41 EB017183).
Special thanks to Orin Mishkit, Zakia Ben Youss Gironda, Orlando Aristizabal, and Youssef Wadghiri at the NYU Langone Health Preclinical Imaging Laboratory for technical assistance.

Keywords

Mouse MRI • Diffusion MRI • MEMRI • Optic Pathways • Visual System • MRtrix3 • ANTs • Preclinical Imaging • Bruker BioSpec • Multi-shell DWI • 7 Tesla MRI

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