1. Identify the mouse to be imaged in its cage and transfer it to the anesthesia induction chamber.
2. Anesthetize the mouse using isoflurane and confirm knockdown using a toe-pinch technique. Take the paw between your thumb and index finger and pinch firmly to check for a response. If the animal withdraws their foot, you should either wait or redose with anesthesia according to the approved protocol.
3. Check that all staff entering the imaging facility are MR safe. This includes removing any magnetic clothing/accessories, confirming no magnetic implants or pacemakers, and removing metal containing piercings.
4. Open isoflurane flow to the nosecone in the MRI room. This allows the longer tubing to be primed with anesthetic before mouse transfer to ensure the animal does not wake up.
5. Close isoflurane flow to the anesthesia induction chamber and transfer the mouse to the imaging stage. Place the mouse on the stage such that the approximate location of the heart is aligned with the center of the magnet.
6. Secure the nose cone and reconfirm knockdown using the toe-pinch technique.
7. Insert the three electrocardiogram leads subcutaneously with one lead to the left and right of the heart and one at the base of the left hind limb.
8. Insert the rectal temperature probe using a sterile probe sheath and lubricant.
9. Place the pillow respiration sensor on the epigastric region of the abdomen and secure it in place using a cardboard plate. The cardboard will allow ensure a pressure-sensitive signal.
10. Confirm all physiological signals are being acquired through the monitoring software outside the scanner room. If a heart rate, respiratory rate, or temperature outside of the normal range is detected, pause imaging and assess whether the animal is appropriately anesthetized. If the animal is found to be in distress, anesthesia administration should cease and the animal should be returned to the cage to recover.
11. Set-up the heating module and fan and begin warming airflow to the animal. Secure all the air tubing in place so that the warm air blows toward the mouse starting just past the tip of the tail.
12. Place the gradient coil over the animal and make sure all cables/tubing are secured.

2. Cardiac Magnetic Resonance Imaging - This section can be adapted for other applications.

1. Tune and match the gradient coil outside the bore of the magnet to ensure the maximal signal is being detected from the subject.
2. Slowly insert the imaging stage into the bore of the magnet such that the animal is positioned directly in the center of the bore. This includes making sure the gradient coil has equal spacing along all radial directions. This is the position where the main magnetic field will be most homogeneous.
3. Run a localizer/navigator scan to confirm the location of the mouse within the scanner. Some segment of the heart should be visualized within all three planes (i.e., axial, sagittal, and coronal). If this is not the case, repeat the process of repositioning the mouse and running localizer/navigation scans until the desired position is achieved.
4. Set-up the parameters for the FLASH sequence. For example: TR/TE = 8.0/2.0 ms, FA = 20°, FOV = 35 x 35 mm, matrix-size = 192 x 192, and NEX = 6. Then, select the external triggering to be "on".
5. On the monitoring software, configure the external triggers such that the MRI sequences are started upon identifying the R-peaks in the cardiac cycles and while respiration is stable during the expiratory phase. As those two conditions are met, the sequence can be serially run and data will be acquired.
6. Prescribe and run an initial FLASH sequence slice in the coronal view such that the slice plane follows the axis from the apex of the heart through the aortic valve. This initial cine loop will provide a two-chamber view of the heart.
7. Referencing the results from the two-chamber view, prescribe and run a new FLASH sequence along the apex-aortic valve axis to visualize a four-chamber view.
8. Finally, prescribe a short-axis slice that is perpendicular to the apex-aortic valve axis approximately halfway through the heart. The papillary muscles should be distinctly visible within the cine loop output at this location.
   1. Additional slices can be acquired parallel to this one to build time-synced volumes of the heart. These volumes are created by concatenating adjacent cine loops in post-processing.
9. Once imaging is completed, transfer acquired data to an appropriate location for analysis and remove the animal from the scanner.