Oct 09, 2025
High-resolution imaging of the human cadaver spinal cord
- Matteo Del Brocco1,
- Lucy Liang1,
- Lee Fisher1,
- T Kevin Hitchens1,
- Elvira Pirondini1
- 1University of Pittsburgh
Protocol Citation: Matteo Del Brocco, Lucy Liang, Lee Fisher, T Kevin Hitchens, Elvira Pirondini 2025. High-resolution imaging of the human cadaver spinal cord. protocols.io https://dx.doi.org/10.17504/protocols.io.bp2l6x86zlqe/v1
Manuscript citation:
Liang et al., SpIC3D imaging for spinal in situ contrast 3D visualization, Cell Reports Methods (2025), https://doi.org/10.1016/j.crmeth.2025.101202
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: September 30, 2023
Last Modified: October 09, 2025
Protocol Integer ID: 88600
Keywords: human, spinal cord, imaging, MRI, DTI, CT, resolution imaging of the human cadaver spinal cord, human cadaver spinal cord, cadaver sample, spinal cord, resolution imaging, tissue sample, prepared tissue sample, human cadaver, imaging
Funders Acknowledgements:
SPARC
Grant ID: OT2OD030537
Abstract
Detailed description of steps to extract and prepared tissue samples to acquire ultra-high resolution images of the human cadaver spinal cord, following a SpIC3D pipeline.
The cadaver sample was obtained from the University of Pittsburgh School of Medicine, protocol approved by University of Pittsburgh CORID, ID: 1070.
Materials
Tissue Sample
- Formalin fixed cadaveric human
Chemicals & Solutions
- 1x Phosphate Buffered Saline
- Sodium Azide (S2002, Sigma Adrich, St. Louis, MO)
- GadavistTM Gadobutrol 1 mmol / mL Injection (Bayer Healthcare, Berlin, Germany)
- Fomblin Y LVAC 16/6
Imaging Equipment
- Vertical-bore 9.4T/72mm Bruker AVANCE AV3 HD MicroImaging System
- Siemens, Prisma 3T
- Flexible coil
- CT Scanner, Epica VIMAGO HU system
Other
- Polycarbonate cylindrical rigid container
- Vacuum pump
- Dissection instruments
Troubleshooting
Sample Preparation
Place the cadaveric specimen in a prone position and identify the desired spinal segments by counting the spinous processes.
Start the dissection with a dorsal incision along the side of the spinous process, and carefully dissect laterally to expose the vertebral column.
Confirm the vertebral segments of interest, based on the insertion of the twelfth rib at the T12 spinal segment, then carefully transect the spinal column at least one vertebra above and below the desired segments with a bone rongeur, sharp blade, and other appropriate cutting tools. Make sure not to pull on the spinal cord during this process or the spinal roots may detach.
Cut the lateral muscles and connective tissue to detach the spinal segment (with bone intact).
Once the spinal segment is detached from the rest of the cadaveric human, trim the muscles (and spinal processes if necessary) until the sample is about 5 cm in diameter.
Put a suture on select spine levels, usually placed on the vertebrae at the center of the desired field of view.
Put the sample next to the ruler on a piece of paper or chuck pad, label the corresponding levels of each vertebra of the sample, and take a picture of the sample to keep as reference.
Imaging Protocol
First, perform high-resolution CT imaging (250 µm resolution) on the sample to obtain good images of the vertebral column.
Submerge the sample in a sealed bag with 1x PBS and 0.3% Azide for at least one week at 4º C. For Cadaver 2, switch to 1x PBS with 0.2% Gadavist for around 1-2 weeks at 4º C (two days before the MR scans, immerse the sample in dH2O + 0.2% Gadavist solution to increase tissue water contents to help restore some T2 relaxation time). The PBS rehydrates the tissue, which is critical for MRI acquisition, and Gadavist increases tissue contrast to reduce imaging time. You can also add 0.3% NaN₃ (Sodium Azide) which will help prevent bacterial growth in the process.
Before acquiring MRI imaging, remove the sample from PBS and drain thoroughly. Submerge the sample in a bag with Fomblin and place upright in a vacuum chamber under vacuum for at least 12 hours to remove air bubbles. Wrap rubber bands around the bagged specimen to reduce the volume of the bag and the required amount of Fomblin. Seal the open end of the bag.
If using a 3T scanner, place the specimen in the MRI scanner with the ventral side down, wrapping a flexible coil around it and making sure it cannot move during the scan time.
If using a 9.4T scanner, place the plastic bag with Fomblin in a polycarbonate cylindrical rigid container, with caudal side down. Make sure to minimize any wrinkles in the bag along the walls of the cylinder as best as possible. This will help to minimize any air/tissue interfaces along the long axis of the sample, helping with shimming the magnetic field and making it as homogeneous as possible for high-resolution imaging.
Center the sample in the field of view (FOV). Find the optimal sequences and parameters, in order to achieve the best images quality possible.
Images sequences and parameters
Specimen 1, 3T: T2 SPACE, sagittal orientation, resolution 0.306x0.306x0.306 mm3, Repetition Time 900 ms, Echo Time 134 ms, Number of Averages 4.
Specimen 2, 3T: T2* FLASH, axial orientation, resolution 0.293x0.293x1 mm3, Repetition Time 20 ms, Echo Time 3.36 ms, Number of Averages 2.
Specimen 2, 9.4T: T2 Turbo RARE, sagittal orientation, resolution 0.13x0.13x0.13 mm3, Repetition Time 800 ms, Echo Time 26 ms, Number of Averages 1.
Specimen 2, 9.4T: Fluorine RARE, sagittal orientation, resolution 0.260x0.260x0.260 mm3, Repetition Time 1500 ms, Echo Time 26 ms, Number of Averages 1.
Specimen 2, 9.4T: Fat enhanced RARE, sagittal orientation, resolution 0.13x0.13x0.13 mm3, Repetition Time 500 ms, Echo Time 40 ms, Number of Averages 1.
Specimen 3, 3T: T2* FLASH, axial orientation, resolution 0.293x0.293x1 mm3, Repetition Time 20 ms, Echo Time 10 ms, Number of Averages 1.
Specimen 3, 3T: T1 vibe, sagittal orientation, resolution 0.293x0.293x0.5 mm3, Repetition Time 8 ms, Echo Time 2.72 ms, Number of Averages 6.
Specimen 4, 3T: T2* FLASH, axial orientation, resolution 0.293x0.293x1 mm3, Repetition Time 20 ms, Echo Time 13 ms, Number of Averages 2.
Specimen 4, 3T: T2* FLASH, axial orientation, resolution 0.293x0.293x1 mm3, Repetition Time 10 ms, Echo Time 3.27 ms, Number of Averages 2.
Specimen 6, 3T: T2* FLASH, axial orientation, resolution 0.293x0.293x1 mm3, Repetition Time 20 ms, Echo Time 3.36 ms, Number of Averages 1.
Note:
- Selective fat excitation and refocusing was achieved with RF frequency at -3.5 ppm.
- Selective fluorine excitation was achieved with RF frequency at -85ppm for Fomblin.