Jacobs: Protocol In vivo microCT scanning protocol for live mice

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In vivo microCT scanning protocol for live mice

(KL and JCC 1/27/2011)

This procedure is best with 2-3 people.

Do not tape anything to the outside of the tube; it will interfere with scanning


  • Scotch tape
  • lab tape
  • scissors
  • gauze
  • flat forceps
  • plastic bag


  1. Bring down the Isoflurane machine and mice from the animal room, Fairchild 1120.
  2. Set up of the scanning bed
    1. Line the right side of the small tube with a layer of gauze (objects at the edge of the tube will be cut off by the scanner) and secure with tape
    2. Slide the nose cone and tubes through the bottom of the platform and then directly through the vice in front of the scanning platform towards the top of the bed (do not secure this yet)
    3. Tape one side of a plastic bag to the edge of the scanning bed- you will flip this over later to cover the mouse’s head and nose cone
    4. Tape a pillow of gauze onto the white holder for the mouse’s head to rest on.
  3. Anesthesia of the rats
    1. Settings: 2-2.5L/min oxygen, 2% Iso for younger mice (older mice can handle 1.5-2 L/min oxygen and 2.5% Iso)
    2. Open the induction chamber valve and close the nose cone valve
    3. Place mouse in induction chamber
    4. After about 2 minutes the mouse should be anesthetized (the tail should no longer balance the mouse when you rock the chamber)
    5. Change the gas channel to the nose cone
  4. In vivo microCT scanning
    1. Place the mouse on a bed of gauze so that it is easy to maneuver it into the scanning tube
    2. Slide the mouse face up into the scanning tube with its tail first, so that his legs are closest to the scanner.
    3. Lean the mouse on the opposite side of your target (for the right tibia, lean it slightly on its left side)
    4. Allow about 1-2 inches between of the mouse’s feet and the end of the tube
    5. Immediately adjust the nose cone so that the mouse’s nose and mouth are completely within it. Then tighten the screw holding the gas tubing in place. Tape down the nose cone. Tape the other end of the plastic bag to cover the mouse and nose cone.
    6. With forceps, reach into the tube and gently pull the mouse’s right foot straight and forward while another person tapes it to the gauze-lined tube
    7. Nudge the mouse’s other foot downwards so that those bones do not get in the way during Scout view
    8. Tape the tail out of the way (or to the top of the tube) using scotch tape
    9. Install the webcam
  5. microCT scanning settings
    1. 15um resolution
    2. Start and end position is 80 and 130 so that the proximal tibia can be maximally exposed
    3. Scout view reference line will be .5 mm distal to the proximal growth plate. Press “OK,” “Scan,” and “Start Measurement”
    4. Scanning duration will be about 10 minutes
    5. During scanning, chest movement should be monitored all the time through the webcam for gasping, meaning a lack of oxygen- adjust oxygen and isoflurane dosage
  6. Once the scanning is done, place the mice back in the cage with a warm light shining on it
  7. After fully recovering from anesthesia, put the animals back in the quarantine animal room, Fairchild 1116.

  • History: KL-JCC, last updated 1/27/11