SBEM imaging, light microscopy imaging and electron microscopy sample preparation were performed with the use of the equipment of Laboratory of Imaging Tissue and Function which serves as an imaging core facility at the Nencki Institute of Experimental Biology.
For preparation of Figure 1, the image of a mouse (Souris_02), and a vial from the https://smart.servier.com/ was used.
This work was supported by the National Science Centre (Poland) Grant Opus (UMO-2018/31/B/NZ4/01603) awarded to KR.

The research was performed in compliance with Nencki Institute guidelines and permission of the Local Ethical Committee. The studies were carried out in accordance with the European Communities Council Directive of 24 November 1986 (86/609/EEC), Animal Protection Act of Poland and approved by the first Local Ethics Committee in Warsaw. All efforts were made to minimize the number of animals used and their suffering.
CAUTION: All procedures described below must be carried out in a laboratory fu...

<ol>
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A., Caly, A., Bernas, T., Radwanska, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neuronal+plasticity+affects+correlation+between+the+size+of+dendritic+spine+and+its+postsynaptic+density.">Neuronal plasticity affects correlation between the size of dendritic spine and its postsynaptic density.</a> Scientific Reports. 9 (1), 1693 (2019).</li><li>Leighton, S. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SEM+images+of+block+faces,+cut+by+a+miniature+microtome+within+the+SEM+-+a+technical+note.">SEM images of block faces, cut by a miniature microtome within the SEM - a technical note.</a> Scanning Electron Microscopy. , 73-76 (1981).</li><li>Denk, W., Horstmann, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Serial+Block-Face+Scanning+Electron+Microscopy+to+Reconstruct+Three-Dimensional+Tissue+Nanostructure.">Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure.</a> PLoS Biology. 2 (11), 329 (2004).</li><li>Smith, D., Starborg, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Serial+block+face+scanning+electron+microscopy+in+cell+biology:+Applications+and+technology.">Serial block face scanning electron microscopy in cell biology: Applications and technology.</a> Tissue and Cell. 57, 111-122 (2019).</li><li>Titze, B., Genoud, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Volume+scanning+electron+microscopy+for+imaging+biological+ultrastructure:+Volume+scanning+electron+microscopy.">Volume scanning electron microscopy for imaging biological ultrastructure: Volume scanning electron microscopy.</a> Biology of the Cell. 108 (11), 307-323 (2016).</li><li>Deerinck, T. J., Bushong, E. A., Thor, A., Ellisman, M. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> NCMIR methods for 3D EM: A new protocol for preparation of biological specimens for serial block face scanning electron microscopy. , 6-8 (2010).</li><li>Willingham, M. C., Rutherford, A. 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C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reconstruct:+a+free+editor+for+serial+section+microscopy.">Reconstruct: a free editor for serial section microscopy.</a> Journal of Microscopy. 218 (1), 52-61 (2005).</li><li>Roels, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+interactive+ImageJ+plugin+for+semi-automated+image+denoising+in+electron+microscopy.">An interactive ImageJ plugin for semi-automated image denoising in electron microscopy.</a> Nature Communications. 11 (1), 771 (2020).</li><li>Radwanska, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanism+for+long-term+memory+formation+when+synaptic+strengthening+is+impaired.">Mechanism for long-term memory formation when synaptic strengthening is impaired.</a> Proceedings of the National Academy of Sciences. 108 (45), 18471-18475 (2011).</li><li>Kittelmann, M., Hawes, C., Hughes, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Serial+block+face+scanning+electron+microscopy+and+the+reconstruction+of+plant+cell+membrane+systems:+SBFSEM+Methods+for+Plant+Cells.">Serial block face scanning electron microscopy and the reconstruction of plant cell membrane systems: SBFSEM Methods for Plant Cells.</a> Journal of Microscopy. 263 (2), 200-211 (2016).</li><li>Fendrych, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Programmed+Cell+Death+Controlled+by+ANAC033/SOMBRERO+Determines+Root+Cap+Organ+Size+in+Arabidopsis.">Programmed Cell Death Controlled by ANAC033/SOMBRERO Determines Root Cap Organ Size in Arabidopsis.</a> Current Biology. 24 (9), 931-940 (2014).</li><li>Russell, M. 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The authors have nothing to disclose.

There are many variations of the primary NCMIR method described by Deerinck in 201010. The basic principles remain the same but, depending on the type of material studied, slight changes are implemented. It was described previously that different resins can be used to embed specimens for SBEM and for example in the case of plants, Spurr&#39;s is the resin of choice due to its low viscosity that allows better infiltration through the cell walls22,<sup class="xref"...

Most of the excitatory synapses in the central nervous system are located on dendritic spines - small protrusions of a neuronal membrane. These protrusions form confined biochemical compartments that control intracellular signal transduction. Structural plasticity of dendritic spines and synapses is closely related to the functional changes in synaptic efficacy that underlie such important processes as learning and memory1,2. It is important to note that electron microscopy (EM) is the only technique that allows to determine if a dendritic spine has a presynaptic input. EM resolution is also needed to study ultrastructural details such as shape of a postsynaptic density (PSD), representing a postsynaptic part of a synapse, or dimensions of a dendritic spine, as well as the size and shape of an axonal bouton. Additionally, with EM it is possible to visualize synapses and their surroundings.
Thanks to advances in imaging and computing technologies it is possible to reconstruct entire neural circuits. Volume electron microscopy techniques, such as serial section transmission electron microscopy (ssTEM), serial block-face scanning electron microscopy (SBEM), and focused ion beam scanning electron microscopy (FIB-SEM) are commonly used for neuronal circuit reconstructions3.
In our studies, the SBEM method is successfully employed to investigate the structural plasticity of dendritic spines and PSDs in samples of the mouse hippocampus and organotypic brain slices 4,5. The SBEM is based on the installation of a miniature ultramicrotome inside the scanning electron microscope chamber6,7,8,9. The top of the sample block is imaged, and then the sample is cut at a specified depth by the ultramicrotome, revealing a new block-face, which is again imaged and then the process is repeated8. As a result, only the image of a block-face is left while the slice which has been cut is lost as debris. That is why SBEM is called a destructive technique, meaning it is not possible to image the same place again. However, the advantage of the destructive on-block methods is that they do not suffer from warping problems and section loss that can significantly affect the data quality and the data analysis3. Moreover, SBEM gives the possibility to image a relatively large field of view ( &#62; 0.5 mm &#215; 0.5 mm) at high resolution3.
To employ SBEM, samples have to be prepared according to a dedicated, highly contrasting protocol due to the backscattered electron detector used for acquiring images. We show here how to perform sample preparation according to the protocol based on a procedure developed by Deerinck10 (National Center for Microscopy and Imaging Research (NCMIR)&#160;method), using reduced osmium-thiocarbohydrazide-osmium (rOTO) stains developed in the 1980s8,11. In addition, we introduce a two-step fixation approach, with mild fixation perfusion that allows to use the same brain both for immunofluorescence studies with light microscopy and SBEM.
In the protocol a mouse brain is primarily fixed with a mild fixative, and then cut into halves, and one hemisphere is postfixed and prepared for immunofluorescence (IF), while the other for EM studies (Figure 1).
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/62712/62712fig01.jpg" /> 
Figure 1. Schematic representation of the workflow for the dendritic spines preparation for the analysis with SBEM. Mice were sacrificed and perfused with a mild primary fixative. The brain was cut into halves, and one hemisphere was postfixed with immunofluorescence (IF)-dedicated fixative, cryoprotected, sliced using a cryostat and processed for IF studies, while the other hemisphere was postfixed with EM fixative, sliced with the vibratome and prepared for EM studies. Brain slices for SBEM studies were contrasted, flat embedded in resin, then a CA1 region of the hippocampus was mounted to the pin, and imaged with SBEM (Figure 1). The part of the protocol highlighted in a yellow box was featured in the video. <a href="https://www.jove.com/files/ftp_upload/62712/62712fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Anesthetic:</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Ketamine/xylazine mixture (Ketamina/Sedazin)</td>
			<td>Biowet Pulawy, Pulawy, Poland</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium pentobarbital (Morbital)</td>
			<td>Biowet Pulawy, Pulawy, Poland</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Fixatives:</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Glutaraldehyde (GA)</td>
			<td>Sigma-Aldrich,St. Louis, MI, USA</td>
			<td>G5882</td>
			<td>Grade I, 25% in H2O, specially purified for use as an electron microscopy fixative</td>
		</tr>
		<tr>
			<td>Hydrochloric acid (HCl)</td>
			<td>POCH, Gliwice, Poland</td>
			<td>575283115</td>
			<td>pure p.a.</td>
		</tr>
		<tr>
			<td>Paraformaldehyde (PFA)</td>
			<td>Sigma-Aldrich,St. Louis, MI, USA</td>
			<td>441244</td>
			<td>prilled, 95%</td>
		</tr>
		<tr>
			<td>Phosphate buffered saline (PBS), pH 7.4</td>
			<td>Sigma-Aldrich,St. Louis, MI, USA</td>
			<td>P4417-50TAB</td>
			<td>tablets</td>
		</tr>
		<tr>
			<td>Sodium hydroxide (NaOH)</td>
			<td>Sigma-Aldrich,St. Louis, MI, USA</td>
			<td>S5881</td>
			<td>reagent grade, <img alt="Equation" src="/files/ftp_upload/62712/62712symbol.png" />98%, pellets (anhydrous)</td>
		</tr>
		<tr>
			<td>Sodium phosphate dibasic (Na2HPO4)</td>
			<td>Sigma-Aldrich,St. Louis, MI, USA</td>
			<td>S3264</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium phosphate monobasic (NaH2PO4)</td>
			<td>Sigma-Aldrich,St. Louis, MI, USA</td>
			<td>S3139</td>
			<td></td>
		</tr>
		<tr>
			<td>Perfusion:</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Large blunt/blunt curved scissors (~14.5 cm)</td>
			<td>Fine Science Tools, Foster City, CA, USA</td>
			<td>14519-14</td>
			<td></td>
		</tr>
		<tr>
			<td>Micro-spatula (double 2&#34; flat ends, one rounded, one tapered to 1/8&#34;)</td>
			<td>Fine Science Tools, Foster City, CA, USA</td>
			<td>10091-12</td>
			<td></td>
		</tr>
		<tr>
			<td>Needle tip, 15 GA, blunt (perfusion needle)</td>
			<td>KD Medical GmbH Hospital Products, Berlin, Germany</td>
			<td>KD-FINE 900413</td>
			<td>1.80 x 40 mm</td>
		</tr>
		<tr>
			<td>Pair of fine (Graefe) tweezers</td>
			<td>Fine Science Tools, Foster City, CA, USA</td>
			<td>11050-10</td>
			<td></td>
		</tr>
		<tr>
			<td>Perfusion pump</td>
			<td>Lead Fluid</td>
			<td>BQ80S</td>
			<td></td>
		</tr>
		<tr>
			<td>Plastic vials</td>
			<td>Profilab, Warsaw, Poland</td>
			<td>534.02</td>
			<td>plastic vials with blue cap for tissue storage, 20 ml, 31 x 48 mm</td>
		</tr>
		<tr>
			<td>Straight iris scissors (~9 cm)</td>
			<td>Fine Science Tools, Foster City, CA, USA</td>
			<td>14058-11</td>
			<td></td>
		</tr>
		<tr>
			<td>Brain slices preparation for EM:</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>12-well plate</td>
			<td>NEST, Rahway, NJ, USA</td>
			<td>712001</td>
			<td></td>
		</tr>
		<tr>
			<td>Cyanoacrylic glue</td>
			<td>Fenedur, Montevideo, Uruguay</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Glass vials</td>
			<td>Electron Microscopy Sciences, Hatfield, PA, USA</td>
			<td>72632</td>
			<td>20 ml Scintillation Vial, a pack of 100</td>
		</tr>
		<tr>
			<td>Pasteur pipette</td>
			<td>VWR, Radnor, PA, USA</td>
			<td>612-4545</td>
			<td>LDPE, disposable, 7.5 ml</td>
		</tr>
		<tr>
			<td>Razor blade</td>
			<td>Wilkinson Sword, London, UK</td>
			<td></td>
			<td>Classic double edge safety razor blades</td>
		</tr>
		<tr>
			<td>Scalpel blade</td>
			<td>Swann-Morton, Sheffield, UK</td>
			<td>No. 20</td>
			<td></td>
		</tr>
		<tr>
			<td>Vibratome</td>
			<td>Leica Microsystems, Vienna, Austria</td>
			<td>Leica VT1000 S</td>
			<td></td>
		</tr>
		<tr>
			<td>Brain slices preparation for IF:</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>96-well plate</td>
			<td>NEST, Rahway, NJ, USA</td>
			<td>701101</td>
			<td></td>
		</tr>
		<tr>
			<td>Criostat</td>
			<td>Leica Microsystems, Vienna, Austria</td>
			<td>Leica CM 1950</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethylene glycol</td>
			<td>Bioshop, Burlington, Canada</td>
			<td>ETH001</td>
			<td></td>
		</tr>
		<tr>
			<td>Low-profile disposable blade 819</td>
			<td>Leica Biosystems Inc., USA</td>
			<td>14035838925</td>
			<td></td>
		</tr>
		<tr>
			<td>Scalpel blade</td>
			<td>Swann-Morton, Sheffield, UK</td>
			<td>No. 20</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium azide (NaN3)</td>
			<td>POCH, Gliwice, Poland</td>
			<td>792770426</td>
			<td></td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>POCH, Gliwice, Poland</td>
			<td>772090110</td>
			<td></td>
		</tr>
		<tr>
			<td>Tissue freezing medium for cryosectioning, OCT-Compound</td>
			<td>Leica Biosystems, Switzerland</td>
			<td>14020108926</td>
			<td></td>
		</tr>
		<tr>
			<td>Immunostaining:</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>24-well plate</td>
			<td>NEST, Rahway, NJ, USA</td>
			<td>702001</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-Post Synaptic Density Protein 95 Antibody</td>
			<td>Merck-Millipore, Burlington, MA, USA</td>
			<td>MAB1598</td>
			<td></td>
		</tr>
		<tr>
			<td>Confocal microscope</td>
			<td>Zeiss, G&#246;ttingen, Germany</td>
			<td></td>
			<td>Zeiss Spinning Disc microscope (63 &#215; oil objective, NA 1.4, pixel size 0.13 &#181;m &#215; 0.13 &#181;m)</td>
		</tr>
		<tr>
			<td>Cover slide</td>
			<td>Menzel Glaser, Braunschweig, Germany</td>
			<td>B-1231</td>
			<td>24 x 60 mm</td>
		</tr>
		<tr>
			<td>Donkey anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 555</td>
			<td>Invitrogen, Carlsbad, CA, USA</td>
			<td>A31570</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluoromount-G Mounting Medium, with DAPI</td>
			<td>Invitrogen, Carlsbad, CA, USA</td>
			<td>00-4959-52</td>
			<td></td>
		</tr>
		<tr>
			<td>Microscope slide</td>
			<td>Thermo Scientific, Waltham, MA, USA</td>
			<td>AGAA00008</td>
			<td>SuperFrost</td>
		</tr>
		<tr>
			<td>Normal donkey serum (NDS)</td>
			<td>Jackson ImmunoResearch Laboratories, West Grove, PA, USA</td>
			<td>017-000-121</td>
			<td></td>
		</tr>
		<tr>
			<td>Shaker</td>
			<td>JWElectronic, Warsaw, Poland</td>
			<td>KL-942</td>
			<td></td>
		</tr>
		<tr>
			<td>TritonT X-100 Reagent Grade</td>
			<td>Bioshop, Burlington, Canada</td>
			<td>TRX506</td>
			<td></td>
		</tr>
		<tr>
			<td>Electron microsocpy sample preparation</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium hexacyanoferrate(II) trihydrate</td>
			<td>POCH, Gliwice, Poland</td>
			<td>746980113</td>
			<td></td>
		</tr>
		<tr>
			<td>Aclar 33C Film</td>
			<td>Electron Microscopy Sciences, Hatfield, PA, USA</td>
			<td>50425</td>
			<td>Fluoropolymer Film embedding sheet</td>
		</tr>
		<tr>
			<td>DMP-30, 2,4,6-Tris(dimethylaminomethyl)phenol</td>
			<td>Sigma-Aldrich,St. Louis, MI, USA</td>
			<td>T58203</td>
			<td>Epoxy embedding medium accelerator</td>
		</tr>
		<tr>
			<td>Durcupan ACM single component A, M</td>
			<td>Sigma-Aldrich,St. Louis, MI, USA</td>
			<td>44611</td>
			<td>Durcupan ACM single component A, M epoxy resin</td>
		</tr>
		<tr>
			<td>Durcupan ACM single component B</td>
			<td>Sigma-Aldrich,St. Louis, MI, USA</td>
			<td>44612</td>
			<td>Durcupan ACM single component B, hardener 964</td>
		</tr>
		<tr>
			<td>Durcupan ACM single component D</td>
			<td>Sigma-Aldrich,St. Louis, MI, USA</td>
			<td>44614</td>
			<td>Durcupan ACM single component D , plasticizer</td>
		</tr>
		<tr>
			<td>Ethyl alcohol absolute</td>
			<td>POCH, Gliwice, Poland</td>
			<td>64-17-5</td>
			<td>Ethyl alcohol absolute 99.8 % pure P.A.-BASIC</td>
		</tr>
		<tr>
			<td>Genlab laboratory oven</td>
			<td>Wolflabs, York, UK</td>
			<td>Mino/18/SS</td>
			<td>Oven Genlab MINO/18/SS 18l volume, no fan circulation, no digital display, standard temperature gradient, standard recovery rate, no timer, 250&#176;C maximum temperature, 240V electrical supply</td>
		</tr>
		<tr>
			<td>L-Aspartic acid</td>
			<td>Sigma-Aldrich,St. Louis, MI, USA</td>
			<td>A-9256</td>
			<td>reagent grade, <img alt="Equation" src="/files/ftp_upload/62712/62712symbol.png" />98% (HPLC)</td>
		</tr>
		<tr>
			<td>Lead (II) nitrate</td>
			<td>Sigma-Aldrich,St. Louis, MI, USA</td>
			<td>467790</td>
			<td><img alt="Equation" src="/files/ftp_upload/62712/62712symbol.png" />99.95% trace metals basis</td>
		</tr>
		<tr>
			<td>Osmium tetroxide</td>
			<td>Sigma-Aldrich,St. Louis, MI, USA</td>
			<td>75632</td>
			<td>for electron microscopy, 4% in H2O</td>
		</tr>
		<tr>
			<td>pH meter</td>
			<td>Elmetron, Zabrze, Poland</td>
			<td>CP-5-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Rotator</td>
			<td>BioSan, J&#243;zef&#243;w, Poland</td>
			<td>Multi Bio RS-24</td>
			<td>rotator Multi Bio RS-24</td>
		</tr>
		<tr>
			<td>Sodium hydroxide (NaOH)</td>
			<td>Sigma-Aldrich,St. Louis, MI, USA</td>
			<td>S5881</td>
			<td>reagent grade, <img alt="Equation" src="/files/ftp_upload/62712/62712symbol.png" />98%, pellets (anhydrous)</td>
		</tr>
		<tr>
			<td>Sunflower mini shaker</td>
			<td>Grant bio, Shepreth,UK</td>
			<td>PD-3D</td>
			<td></td>
		</tr>
		<tr>
			<td>Syringe filter</td>
			<td>Millipore, Burlington, MA, USA</td>
			<td>SLGP033NB</td>
			<td>0,22 &#181;m pore size</td>
		</tr>
		<tr>
			<td>Thiocarbohydrazide</td>
			<td>Sigma-Aldrich,St. Louis, MI, USA</td>
			<td>88535</td>
			<td>purum p.a., for electron microscopy, <img alt="Equation" src="/files/ftp_upload/62712/62712symbol.png" />99.0% (N)</td>
		</tr>
		<tr>
			<td>Uranyl acetate</td>
			<td>Serva, Heidelberg, Germany</td>
			<td>77870</td>
			<td>Uranyl acetate&#183;2H2O, research grade</td>
		</tr>
		<tr>
			<td>Water bath</td>
			<td>WSL, Swietochlowice, Poland</td>
			<td>LWT</td>
			<td></td>
		</tr>
		<tr>
			<td>Specimen mounting for SBEM</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>96-well culture plate</td>
			<td>VWR, Radnor, PA, USA</td>
			<td>734-2782</td>
			<td>96-well plates, round bottom, non treated</td>
		</tr>
		<tr>
			<td>AM Gatan 3View stub handling tweezers</td>
			<td>Micro to Nano, Haarlem, Netherlands 
			Netherlands</td>
			<td>50-001521</td>
			<td></td>
		</tr>
		<tr>
			<td>Binocular</td>
			<td>OPTA-TECH, Warsaw, Poland</td>
			<td>X2000</td>
			<td></td>
		</tr>
		<tr>
			<td>Conductive glue</td>
			<td>Chemtronics, Georgia, USA</td>
			<td>CW2400</td>
			<td>conductive eopxy</td>
		</tr>
		<tr>
			<td>Gatan 3View sample pin stubs</td>
			<td>Micro to Nano, Haarlem, Netherlands 
			Netherlands</td>
			<td>10-006003</td>
			<td></td>
		</tr>
		<tr>
			<td>Parafilm</td>
			<td>Sigma-Aldrich,St. Louis, MI, USA</td>
			<td>P7793</td>
			<td>roll size 20&#160;in. &#215; 50&#160;ft</td>
		</tr>
		<tr>
			<td>Pelco conductive silver paint</td>
			<td>Ted Pella, Redding, CA, USA</td>
			<td>16062-15</td>
			<td>PELCO&#174;&#160;Conductive Silver Paint, 15g</td>
		</tr>
		<tr>
			<td>Razor blades double edge</td>
			<td>Electron Microscopy Sciences, Hatfield, PA, USA</td>
			<td>72000</td>
			<td>Stainless Steel &#34;PTFE&#34; coated. PERSONNA brand .004&#34; thick, wrapped individually, 250 blades in a box.</td>
		</tr>
		<tr>
			<td>Scanning Electron Microscope</td>
			<td>Zeiss, Oberkochen, Germany</td>
			<td></td>
			<td>Sigma VP with Gatan 3View2 chamber, acceleration voltage 2.5 kV, variable pressure 5 Pa, aperture 20 &#181;m, dwell time 6 &#181;s, slice thickness 60 nm, magnification 15 000 x, image resolution 2048 x 2048 pixels, pixel size 7.3 nm</td>
		</tr>
		<tr>
			<td>trim 90&#176; diamond knife</td>
			<td>Diatome Ltd., Nidau, Switzerland</td>
			<td>DTB90</td>
			<td></td>
		</tr>
		<tr>
			<td>Ultramicrotome</td>
			<td>Leica Microsystems, Vienna, Austria</td>
			<td>Leica ultracutR</td>
			<td></td>
		</tr>
		<tr>
			<td>Software</td>
			<td>webpage</td>
			<td></td>
			<td>tutorials</td>
		</tr>
		<tr>
			<td>FijiJ</td>
			<td>https://fiji.sc/</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Microscopy Image Browser</td>
			<td>http://mib.helsinki.fi/</td>
			<td></td>
			<td>http://mib.helsinki.fi/tutorials.html</td>
		</tr>
		<tr>
			<td>Reconstruct</td>
			<td>https://synapseweb.clm.utexas.edu/software-0</td>
			<td></td>
			<td>https://synapseweb.clm.utexas.edu/software-0)</td>
		</tr>
		<tr>
			<td>Animals</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Mice</td>
			<td>Adult 3-month old and&#160;20&#177;1&#160;month old&#160;female&#160;Thy1-GFP(M) mice (Thy1-GFP +/-) (Feng et al.,2000) which express GFP in a sparsely distributed population of glutamatergic neurons. Animals were bred as heterozygotes with the C57BL/6J background in the Animal House of the Nencki Institute of Experimental Biology.</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

serial block-face scanning electron microscopy (sbem) for the study of dendritic spines

Three-dimensional electron microscopy (3D EM) gives a possibility to analyze morphological parameters of dendritic spines with nanoscale resolution. In addition, some features of dendritic spines, such as volume of the spine and post-synaptic density (PSD) (representing post-synaptic part of the synapse), presence of presynaptic terminal, and smooth endoplasmic reticulum or atypical form of PSD (e.g., multi-innervated spines), can be observed only with 3D EM. By employing serial block-face scanning electron microscopy (SBEM) it is possible to obtain 3D EM data easier and in a more reproducible manner than when performing traditional serial sectioning. Here we show how to prepare mouse hippocampal samples for SBEM analysis and how this protocol can be combined with immunofluorescence study of dendritic spines. Mild fixation perfusion allows us to perform immunofluorescence studies with light microscopy on one half of the brain, while the other half was prepared for SBEM. This approach reduces the number of animals to be used for the study.

Using the method described above high contrast, good resolution images of the mouse brain tissue can be obtained. A large field of view provided by the SBEM technique facilitates precise selection of the region of interest. The large image of the CA1 region of the hippocampus was taken to measure the length of stratum radiatum (SR) (Figure 2A) and to set the imaging precisely in the center (Figure 2B). Next, the stack of images was acquired and the obje...

Watch this Scientific Journal Video about Serial Block-Face Scanning Electron Microscopy SBEM for the Study of Dendritic Spines at JoVE.com

Serial Block-Face Scanning Electron Microscopy SBEM for the Study of Dendritic Spines

Serial Block-Face Scanning Electron Microscopy (SBEM) is applied to image and analyze dendritic spines in the murine hippocampus.

Serial Block-Face Scanning Electron Microscopy (SBEM) for the Study of Dendritic Spines

Three-dimensional electron microscopy (3D EM) gives a possibility to analyze morphological parameters of dendritic spines with nanoscale resolution. In ...

Each neuron in the brain is connected with other neuronal cells by approximately 7, 000 synapses. Except that those synapses in the mammalian brain are chiefly located on the small protrusions of the membrane called dendritic spines. Plasticity of the synapses and dendritic spines and the like, such important brain functions as learning and memory processes.It is important to note that only electron microscopy gives a full insight whether a dendritic spine has a postsynaptic input. Various techniques on dendritic spines imaging are available. However, serial block face scanning electron microscopy gives unique possibility to image large volume of tissue with a high resolution.Serial block-based scanning electron microscopy technique requires a special protocol of sample preparation which involves strong contrasting with heavy metals. My primary fixation during perfusion allowed us to use the same brains for lightened electron microscopy. Mice were sacrificed and perfused with a mild primary fixative.The brain was cut into halves and one hemisphere was post fixed with immunofluorescence dedicated fixative, cryoprotectant, sliced using a cryostat and processed for immunofluorescence studies. Where the other hemisphere was post fixed with electron microscopy fixative, sliced with the vibratome and prepared for electron microscopy studies. Brain slices for serial block-based scanning electron microscopy studies were contrasted, flat embedded in resin, then a CA1 region of the hippocampus was mounted to the pin and imaged with the serial block-based scanning electron microscope.The part of the protocol highlighted in a yellow box was featured in the video. Take the tissue, which has been fixed and cut into 100 microbiotic slices and wash it with cold phosphate buffer five times for three minutes each. Prepare a one-to-one mixture of 4%osmium tetroxide and 3%potassium ferrocyanide.The final product will turn brown. Immerse the samples in this mixture. Then place the samples on ice.And from this stage onwards it's important to protect them from light. Incubate them with gentle shaking for one hour. Meanwhile, prepare the TCH solution.Mix 10 milliliter of double distilled water and 0.1 gram of TCH. Place it into an oven set at 60 Celsius for one hour. It is important to swill the solution from time to time.When ready, cool it to the room temperature. Now wash the samples with double distilled water five times for three minutes each and then immerse them in filtered TCH solution. The slices will turn black.Incubate them for 20 minutes at room temperature. Wash the samples with double distilled water five times for three minutes each and incubate them with 2%osmium tetroxide for 30 minutes, this time at room temperature. Again, wash the samples with double distilled water five times for three minutes each and place them into filtered 1%or amyl acetate.Incubate them at four degrees Celsius overnight. Next day, begin with D-aspartate preparation. Mix lead nitrate with aspartic acid solution pre-warmed to 60 degrees Celsius.Place the mixture in a water bath set at 60 degrees Celsius and adjust the pH to 5.5 with one molar sodium hydroxide. Close the vial with lead aspartate and leave it in 60 degrees Celsius for 30 minutes. The solution should be clear.If it turns cloudy it must be discarded and a new one needs to be prepared. In the meantime, wash the samples with the gas double distilled water five times for three minutes each and keep them in the oven at 60 degrees Celsius for 30 minutes. Immerse the samples in the freshly prepared lead aspartate solution and incubate them in the oven set at 60 degrees Celsius for 20 minutes.Prepare epoxy resin. Weigh the ingredients and mix the resin well for at least 30 minutes before adding accelerator DMP 30. Prepare virus with graded dilution of ethanol.Then take the samples out of the oven and wash them again with double distilled water five times for three minutes each. In the meantime, mix the resin with 100%ethanol in one-to-one proportion to obtain the 50%resin. Mix it well.Following this, dehydrate the samples in each dilution of ethanol for five minutes. Remember the samples must never dry completely. Infiltrate the samples first in 50%resin for 30 minutes, next in 100%resin for one hour, and then again in a fresh 100%resin overnight.The next day, place the samples in fresh 100%resin for one hour and then embed them between fluoropolymer embedding sheets. Prepare pieces of embedding sheet which have been de-greased with ethanol and put aside the glass slides which will be used as support. Place a piece of embedding sheet on a glass slide, put a drop of resin on it, then transfer the sample carefully with the use of wooden stick.Cover it with the second piece. Try to avoid air bubbles. Be gentle as the tissue is very fragile.Carefully place another glass slide on top of the embedding sheet piece and cure the sample in the oven at 70 degrees Celsius for at least 48 hours. Separate the layers and cut a piece of the embedded sample with a razor blade. Transfer it to paraffin.This will minimize the danger of losing the sample due to electrostatics. Take an aluminum pin that has been de-greased with ethanol. Mix a conductive epoxy well and use a little amount of it to mount the sample to the pin.Cure conductive epoxy at 70 degrees Celsius for 10 minutes. Trim each side of the sample block with the diamond knife and then polish the face of the block until the tissue is exposed. Ground the sample to the pin using conductive paint and cure it.To minimize charging, the samples should be also spotted coated with a thin layer of gold or gold palladium. Place the pin with the sample into the chamber of the serial block-based scanning electron microscope. Align the sample to the knife and then close the chamber and set the parameters.Collect a stack of images. Using the described method, images of mouse brain tissue were obtained. The large image of the hippocampus one region was taken and the imaging was set in the center of stratum radiatum.A stack of images was acquired and the objects of interest, such as dendritic spines and synapses, were segmented. Good quality tissue morphology was obtained with clearly visible membranes and synaptic vesicles and well-preserved mitochondria. Immunofluorescent studies of PSD 95 antibody confirmed that mild primary fixation and traditional fixation with 4%PFA give comparable results.Presented protocol enables acquisition of brain tissue images with the use of serial block-based scanning electron microscopy, high-quality tissue morphology, and 12 visible membranes facilitate 10 right segmentation and reconstruction. My primary fixation made it possible to use the same brains for analysis of PSD 95 immunofluorescence and electron microscopy imaging dendritic spines. Here we use PSE 9, 500 budding.However, the other can be used as well.

serial-block-face-scanning-electron-microscopy-sbem-for-study

Research

JoVE Journal

Neuroscience

3.5K Views.  Nencki Institute of Experimental Biology of Polish Academy of Sciences. Each neuron in the brain is connected with other neuronal cells by approximately 7, 000 synapses. Except that those synapses in the mammalian brain are chiefly located on the small protrusions of the membrane called dendritic spines. Plasticity of the synapses and dendritic spines and the like, such important brain functions as learning and memory processes.It is important to note that only electron microscopy gives a full insight whether a dendritic spine has a postsynaptic input. Var...