Semiautomated correlative 3D electron microscopy of in vivo-imaged axons and dendrites.
This protocol describes how in vivo-imaged dendrites and axons in adult mouse brains can subsequently be prepared and imaged with focused ion beam scanning electron microscopy (FIBSEM). The procedure starts after in vivo imaging with chemical fixation, followed by the identification of the fluorescent structures of interest. Their position is then highlighted in the fixed tissue by burning fiducial marks with the two-photon laser. Once the section has been stained and resin-embedded, a small block is trimmed close to these marks. Serially aligned EM images are acquired through this region, using FIBSEM, and the neurites of interest are then reconstructed semiautomatically by using the ilastik software (http://ilastik.org/). This reliable imaging and reconstruction technique avoids the use of specific labels to identify the structures of interest in the electron microscope, enabling optimal chemical fixation techniques to be applied and providing the best possible structural preservation for 3D analysis. The entire protocol takes ∼4 d.
1] BioEM Facility, Centre of Electron Microscopy, EPFL, Lausanne, Switzerland. [2] CV Laboratory, EPFL, Lausanne, Switzerland.
Bohumil
B
Maco
BioEM Facility, Centre of Electron Microscopy, EPFL, Lausanne, Switzerland.
Marco
M
Cantoni
Department of Neuroscience, University Medical Center (CMU), University of Geneva, Geneva, Switzerland.
Anthony
A
Holtmaat
Heidelberg Collaboratory for Image Processing (HCI), University of Heidelberg, Heidelberg, Germany.
Anna
A
Kreshuk
Heidelberg Collaboratory for Image Processing (HCI), University of Heidelberg, Heidelberg, Germany.
Fred A
FA
Hamprecht
BioEM Facility, Centre of Electron Microscopy, EPFL, Lausanne, Switzerland.
Graham W
GW
Knott
D000818:Animals; D001369:Axons / Q000648:ultrastructure*; D001921:Brain / Q000166:cytology*; D003712:Dendrites / Q000648:ultrastructure*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D007834:Lasers; D051379:Mice; D008855:Microscopy, Electron, Scanning / Q000379:methods*; D012984:Software