https://wiki.eyewire.org/index.php?title=index.php&&title=Serial_block-face_scanning_electron_microscopy_(SBFSEM)&feed=atom&action=historySerial block-face scanning electron microscopy (SBFSEM) - Revision history2024-03-29T10:59:57ZRevision history for this page on the wikiMediaWiki 1.25.2https://wiki.eyewire.org/index.php?title=Serial_block-face_scanning_electron_microscopy_(SBFSEM)&diff=10720&oldid=prevNkem test: Marked this version for translation2016-06-14T18:23:14Z<p>Marked this version for translation</p>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><!--T:1--></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Serial block-face scanning electron microscopy (SBFSEM) is a method for generating high resolution 3D images from biological samples. It was created at the Max Planck Institute in Germany, specifically for the purpose of imaging neurons.<ref name="Denk">Denk W, Horstmann H (2004) Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure. PLoS Biol 2(11): e329. doi:[http://dx.doi.org/10.1371/journal.pbio.0020329 10.1371/journal.pbio.0020329]</ref></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Serial block-face scanning electron microscopy (SBFSEM) is a method for generating high resolution 3D images from biological samples. It was created at the Max Planck Institute in Germany, specifically for the purpose of imaging neurons.<ref name="Denk">Denk W, Horstmann H (2004) Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure. PLoS Biol 2(11): e329. doi:[http://dx.doi.org/10.1371/journal.pbio.0020329 10.1371/journal.pbio.0020329]</ref></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>===How EyeWire uses SBFSEM===</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>===How EyeWire uses SBFSEM=== <ins class="diffchange diffchange-inline"><!--T:2--></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><!--T:3--></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The images you see on EyeWire come to us from our collaborators Kevin Briggman, Moritz Helmstaedter, and Winfried Denk at the Max Planck Institute in Germany, and the dataset is called [[e2198]].</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The images you see on EyeWire come to us from our collaborators Kevin Briggman, Moritz Helmstaedter, and Winfried Denk at the Max Planck Institute in Germany, and the dataset is called [[e2198]].</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><!--T:4--></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Before any imaging could be done, the sample was stained with heavy metals. When the scanning electron microscope's electrons collided with the heavy metals in the sample, they would bounce off and they would be collected by a detector. These electrons that bounce off the sample are known as backscattered electrons. After being placed inside the chamber of the microscope, the surface of the sample is imaged. Because the Scanning Electron Microscope uses a tightly focused beam of electrons, the sample needs to be scanned in a certain pattern. The Scanning Electron Microscope will move across a line, scanning it one piece at a time, and then it will move onto the next line. This is known as raster-scanning.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Before any imaging could be done, the sample was stained with heavy metals. When the scanning electron microscope's electrons collided with the heavy metals in the sample, they would bounce off and they would be collected by a detector. These electrons that bounce off the sample are known as backscattered electrons. After being placed inside the chamber of the microscope, the surface of the sample is imaged. Because the Scanning Electron Microscope uses a tightly focused beam of electrons, the sample needs to be scanned in a certain pattern. The Scanning Electron Microscope will move across a line, scanning it one piece at a time, and then it will move onto the next line. This is known as raster-scanning.</div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><!--T:5--></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>After the entire surface of the sample has been imaged, an [[Ultramicrotome| ultramicrotome]] slices off the surface of the sample and the underlying surface is then imaged in the same way. The images from the scans of each successive layer of the sample were combined to form a 3D dataset.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>After the entire surface of the sample has been imaged, an [[Ultramicrotome| ultramicrotome]] slices off the surface of the sample and the underlying surface is then imaged in the same way. The images from the scans of each successive layer of the sample were combined to form a 3D dataset.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><!--T:6--></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Think of the the stack of 2D images like a [http://en.wikipedia.org/wiki/Flip_book flip book].The way flip books work is that from one page to another there is a small change in the drawing, and several small changes in a row create the action in the flip book.  The 2D image you see in EyeWire is like one single page from a flip book.  The 2D is static, but when you scroll through the slices you can see the change from one slice of retina (or page of a flip book) to another.  The idea is that if you follow the shape of one neuron from one 2D slice to the next, coloring each piece as you go, you can eventually discern the shape of the neuron in the 3D.  Each piece you color in the 2D builds upon the previous one.  It's like stacking blocks, each layer of blocks is flat, but as you continue stacking the blocks on top of each other you eventually get a 3D shape.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Think of the the stack of 2D images like a [http://en.wikipedia.org/wiki/Flip_book flip book].The way flip books work is that from one page to another there is a small change in the drawing, and several small changes in a row create the action in the flip book.  The 2D image you see in EyeWire is like one single page from a flip book.  The 2D is static, but when you scroll through the slices you can see the change from one slice of retina (or page of a flip book) to another.  The idea is that if you follow the shape of one neuron from one 2D slice to the next, coloring each piece as you go, you can eventually discern the shape of the neuron in the 3D.  Each piece you color in the 2D builds upon the previous one.  It's like stacking blocks, each layer of blocks is flat, but as you continue stacking the blocks on top of each other you eventually get a 3D shape.</div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><!--T:7--></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>For a less technical explanation you can view the [http://blog.eyewire.org/behind-the-science-about-the-data/ article] on the blog.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>For a less technical explanation you can view the [http://blog.eyewire.org/behind-the-science-about-the-data/ article] on the blog.</div></td></tr>
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</table>Nkem testhttps://wiki.eyewire.org/index.php?title=Serial_block-face_scanning_electron_microscopy_(SBFSEM)&diff=10434&oldid=prevIgxae2357: Undo revision 10433 by Igxae2357 (talk)2016-06-09T16:10:19Z<p>Undo revision 10433 by <a href="/Special:Contributions/Igxae2357" title="Special:Contributions/Igxae2357">Igxae2357</a> (<a href="/index.php?title=User_talk:Igxae2357&action=edit&redlink=1" class="new" title="User talk:Igxae2357 (page does not exist)">talk</a>)</p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Serial block-face scanning electron microscopy (SBFSEM) is a method for generating high resolution 3D images from biological samples. It was created at the Max Planck Institute in Germany, specifically for the purpose of imaging neurons.<ref name="Denk">Denk W, Horstmann H (2004) Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure. PLoS Biol 2(11): e329. doi:[http://dx.doi.org/10.1371/journal.pbio.0020329 10.1371/journal.pbio.0020329]</ref></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Serial block-face scanning electron microscopy (SBFSEM) is a method for generating high resolution 3D images from biological samples. It was created at the Max Planck Institute in Germany, specifically for the purpose of imaging neurons.<ref name="Denk">Denk W, Horstmann H (2004) Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure. PLoS Biol 2(11): e329. doi:[http://dx.doi.org/10.1371/journal.pbio.0020329 10.1371/journal.pbio.0020329]</ref></div></td></tr>
</table>Igxae2357https://wiki.eyewire.org/index.php?title=Serial_block-face_scanning_electron_microscopy_(SBFSEM)&diff=10433&oldid=prevIgxae2357 at 16:09, 9 June 20162016-06-09T16:09:54Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Serial block-face scanning electron microscopy (SBFSEM) is a method for generating high resolution 3D images from biological samples. It was created at the Max Planck Institute in Germany, specifically for the purpose of imaging neurons.<ref name="Denk">Denk W, Horstmann H (2004) Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure. PLoS Biol 2(11): e329. doi:[http://dx.doi.org/10.1371/journal.pbio.0020329 10.1371/journal.pbio.0020329]</ref></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Serial block-face scanning electron microscopy (SBFSEM) is a method for generating high resolution 3D images from biological samples. It was created at the Max Planck Institute in Germany, specifically for the purpose of imaging neurons.<ref name="Denk">Denk W, Horstmann H (2004) Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure. PLoS Biol 2(11): e329. doi:[http://dx.doi.org/10.1371/journal.pbio.0020329 10.1371/journal.pbio.0020329]</ref></div></td></tr>
</table>Igxae2357https://wiki.eyewire.org/index.php?title=Serial_block-face_scanning_electron_microscopy_(SBFSEM)&diff=10364&oldid=prevPilnpat at 14:21, 9 June 20162016-06-09T14:21:25Z<p></p>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><languages /></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><translate></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Serial block-face scanning electron microscopy (SBFSEM) is a method for generating high resolution 3D images from biological samples. It was created at the Max Planck Institute in Germany, specifically for the purpose of imaging neurons.<ref name="Denk">Denk W, Horstmann H (2004) Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure. PLoS Biol 2(11): e329. doi:[http://dx.doi.org/10.1371/journal.pbio.0020329 10.1371/journal.pbio.0020329]</ref></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Serial block-face scanning electron microscopy (SBFSEM) is a method for generating high resolution 3D images from biological samples. It was created at the Max Planck Institute in Germany, specifically for the purpose of imaging neurons.<ref name="Denk">Denk W, Horstmann H (2004) Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure. PLoS Biol 2(11): e329. doi:[http://dx.doi.org/10.1371/journal.pbio.0020329 10.1371/journal.pbio.0020329]</ref></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><references /></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><references /></div></td></tr>
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</table>Pilnpathttps://wiki.eyewire.org/index.php?title=Serial_block-face_scanning_electron_microscopy_(SBFSEM)&diff=2929&oldid=prevDannyS at 14:03, 7 August 20142014-08-07T14:03:57Z<p></p>
<table class='diff diff-contentalign-left'>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 14:03, 7 August 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="L5" >Line 5:</td>
<td colspan="2" class="diff-lineno">Line 5:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The images you see on EyeWire come to us from our collaborators Kevin Briggman, Moritz Helmstaedter, and Winfried Denk at the Max Planck Institute in Germany, and the dataset is called [[e2198]].</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The images you see on EyeWire come to us from our collaborators Kevin Briggman, Moritz Helmstaedter, and Winfried Denk at the Max Planck Institute in Germany, and the dataset is called [[e2198]].</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Before any imaging could be done, the sample was <del class="diffchange diffchange-inline">coated </del>with heavy metals. When the scanning electron microscope's electrons collided with the heavy metals in the sample, they would bounce off and they would be collected by a detector. These electrons that bounce off the sample are known as backscattered electrons. After being placed inside the chamber of the microscope, the surface of the sample is imaged. Because the Scanning Electron Microscope uses a tightly focused beam of electrons, the sample needs to be scanned in a certain pattern. The Scanning Electron Microscope will move across a line, scanning it one piece at a time, and then it will move onto the next line. This is known as raster-scanning.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Before any imaging could be done, the sample was <ins class="diffchange diffchange-inline">stained </ins>with heavy metals. When the scanning electron microscope's electrons collided with the heavy metals in the sample, they would bounce off and they would be collected by a detector. These electrons that bounce off the sample are known as backscattered electrons. After being placed inside the chamber of the microscope, the surface of the sample is imaged. Because the Scanning Electron Microscope uses a tightly focused beam of electrons, the sample needs to be scanned in a certain pattern. The Scanning Electron Microscope will move across a line, scanning it one piece at a time, and then it will move onto the next line. This is known as raster-scanning.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>After the entire surface of the sample has been imaged, an [[Ultramicrotome| ultramicrotome]] slices off the surface of the sample and the underlying surface is then imaged in the same way. The images from the scans of each successive layer of the sample were combined to form a 3D dataset.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>After the entire surface of the sample has been imaged, an [[Ultramicrotome| ultramicrotome]] slices off the surface of the sample and the underlying surface is then imaged in the same way. The images from the scans of each successive layer of the sample were combined to form a 3D dataset.</div></td></tr>
</table>DannyShttps://wiki.eyewire.org/index.php?title=Serial_block-face_scanning_electron_microscopy_(SBFSEM)&diff=2671&oldid=prevDannyS at 18:09, 20 June 20142014-06-20T18:09:13Z<p></p>
<table class='diff diff-contentalign-left'>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 18:09, 20 June 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="L7" >Line 7:</td>
<td colspan="2" class="diff-lineno">Line 7:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Before any imaging could be done, the sample was coated with heavy metals. When the scanning electron microscope's electrons collided with the heavy metals in the sample, they would bounce off and they would be collected by a detector. These electrons that bounce off the sample are known as backscattered electrons. After being placed inside the chamber of the microscope, the surface of the sample is imaged. Because the Scanning Electron Microscope uses a tightly focused beam of electrons, the sample needs to be scanned in a certain pattern. The Scanning Electron Microscope will move across a line, scanning it one piece at a time, and then it will move onto the next line. This is known as raster-scanning.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Before any imaging could be done, the sample was coated with heavy metals. When the scanning electron microscope's electrons collided with the heavy metals in the sample, they would bounce off and they would be collected by a detector. These electrons that bounce off the sample are known as backscattered electrons. After being placed inside the chamber of the microscope, the surface of the sample is imaged. Because the Scanning Electron Microscope uses a tightly focused beam of electrons, the sample needs to be scanned in a certain pattern. The Scanning Electron Microscope will move across a line, scanning it one piece at a time, and then it will move onto the next line. This is known as raster-scanning.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>After the entire surface of the sample has been imaged, <del class="diffchange diffchange-inline">a vibratome </del>slices off the surface of the sample and the underlying surface is then imaged in the same way. The images from the scans of each successive layer of the sample were combined to form a 3D dataset.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>After the entire surface of the sample has been imaged, <ins class="diffchange diffchange-inline">an [[Ultramicrotome| ultramicrotome]] </ins>slices off the surface of the sample and the underlying surface is then imaged in the same way. The images from the scans of each successive layer of the sample were combined to form a 3D dataset.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Think of the the stack of 2D images like a [http://en.wikipedia.org/wiki/Flip_book flip book].The way flip books work is that from one page to another there is a small change in the drawing, and several small changes in a row create the action in the flip book.  The 2D image you see in EyeWire is like one single page from a flip book.  The 2D is static, but when you scroll through the slices you can see the change from one slice of retina (or page of a flip book) to another.  The idea is that if you follow the shape of one neuron from one 2D slice to the next, coloring each piece as you go, you can eventually discern the shape of the neuron in the 3D.  Each piece you color in the 2D builds upon the previous one.  It's like stacking blocks, each layer of blocks is flat, but as you continue stacking the blocks on top of each other you eventually get a 3D shape.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Think of the the stack of 2D images like a [http://en.wikipedia.org/wiki/Flip_book flip book].The way flip books work is that from one page to another there is a small change in the drawing, and several small changes in a row create the action in the flip book.  The 2D image you see in EyeWire is like one single page from a flip book.  The 2D is static, but when you scroll through the slices you can see the change from one slice of retina (or page of a flip book) to another.  The idea is that if you follow the shape of one neuron from one 2D slice to the next, coloring each piece as you go, you can eventually discern the shape of the neuron in the 3D.  Each piece you color in the 2D builds upon the previous one.  It's like stacking blocks, each layer of blocks is flat, but as you continue stacking the blocks on top of each other you eventually get a 3D shape.</div></td></tr>
</table>DannyShttps://wiki.eyewire.org/index.php?title=Serial_block-face_scanning_electron_microscopy_(SBFSEM)&diff=2584&oldid=prevDannyS at 16:54, 17 June 20142014-06-17T16:54:31Z<p></p>
<table class='diff diff-contentalign-left'>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 16:54, 17 June 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="L1" >Line 1:</td>
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<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Serial block-face scanning electron microscopy (SBFSEM) is a method for generating high resolution 3D images from biological samples. It was created at the Max Planck Institute in Germany, specifically for the purpose of imaging neurons.<ref name="Denk">Denk W, Horstmann H (2004) Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure. PLoS Biol 2(11): e329. doi:10.1371/journal.pbio.0020329</ref></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Serial block-face scanning electron microscopy (SBFSEM) is a method for generating high resolution 3D images from biological samples. It was created at the Max Planck Institute in Germany, specifically for the purpose of imaging neurons.<ref name="Denk">Denk W, Horstmann H (2004) Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure. PLoS Biol 2(11): e329. doi:<ins class="diffchange diffchange-inline">[http://dx.doi.org/10.1371/journal.pbio.0020329 </ins>10.1371/journal.pbio.0020329<ins class="diffchange diffchange-inline">]</ins></ref></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>===How EyeWire uses SBFSEM===</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>===How EyeWire uses SBFSEM===</div></td></tr>
</table>DannyShttps://wiki.eyewire.org/index.php?title=Serial_block-face_scanning_electron_microscopy_(SBFSEM)&diff=2536&oldid=prevDannyS at 16:17, 16 June 20142014-06-16T16:17:00Z<p></p>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 16:17, 16 June 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="L11" >Line 11:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Think of the the stack of 2D images like a [http://en.wikipedia.org/wiki/Flip_book flip book].The way flip books work is that from one page to another there is a small change in the drawing, and several small changes in a row create the action in the flip book.  The 2D image you see in EyeWire is like one single page from a flip book.  The 2D is static, but when you scroll through the slices you can see the change from one slice of retina (or page of a flip book) to another.  The idea is that if you follow the shape of one neuron from one 2D slice to the next, coloring each piece as you go, you can eventually discern the shape of the neuron in the 3D.  Each piece you color in the 2D builds upon the previous one.  It's like stacking blocks, each layer of blocks is flat, but as you continue stacking the blocks on top of each other you eventually get a 3D shape.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Think of the the stack of 2D images like a [http://en.wikipedia.org/wiki/Flip_book flip book].The way flip books work is that from one page to another there is a small change in the drawing, and several small changes in a row create the action in the flip book.  The 2D image you see in EyeWire is like one single page from a flip book.  The 2D is static, but when you scroll through the slices you can see the change from one slice of retina (or page of a flip book) to another.  The idea is that if you follow the shape of one neuron from one 2D slice to the next, coloring each piece as you go, you can eventually discern the shape of the neuron in the 3D.  Each piece you color in the 2D builds upon the previous one.  It's like stacking blocks, each layer of blocks is flat, but as you continue stacking the blocks on top of each other you eventually get a 3D shape.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>For a less technical explanation you can view the <del class="diffchange diffchange-inline">[</del>[http://blog.eyewire.org/behind-the-science-about-the-data/ article<del class="diffchange diffchange-inline">]</del>] on the blog</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>For a less technical explanation you can view the [http://blog.eyewire.org/behind-the-science-about-the-data/ article] on the blog<ins class="diffchange diffchange-inline">.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><references /></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><references /></div></td></tr>
</table>DannyShttps://wiki.eyewire.org/index.php?title=Serial_block-face_scanning_electron_microscopy_(SBFSEM)&diff=2535&oldid=prevDannyS at 16:16, 16 June 20142014-06-16T16:16:48Z<p></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
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<col class='diff-marker' />
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<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 16:16, 16 June 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="L10" >Line 10:</td>
<td colspan="2" class="diff-lineno">Line 10:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Think of the the stack of 2D images like a [http://en.wikipedia.org/wiki/Flip_book flip book].The way flip books work is that from one page to another there is a small change in the drawing, and several small changes in a row create the action in the flip book.  The 2D image you see in EyeWire is like one single page from a flip book.  The 2D is static, but when you scroll through the slices you can see the change from one slice of retina (or page of a flip book) to another.  The idea is that if you follow the shape of one neuron from one 2D slice to the next, coloring each piece as you go, you can eventually discern the shape of the neuron in the 3D.  Each piece you color in the 2D builds upon the previous one.  It's like stacking blocks, each layer of blocks is flat, but as you continue stacking the blocks on top of each other you eventually get a 3D shape.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Think of the the stack of 2D images like a [http://en.wikipedia.org/wiki/Flip_book flip book].The way flip books work is that from one page to another there is a small change in the drawing, and several small changes in a row create the action in the flip book.  The 2D image you see in EyeWire is like one single page from a flip book.  The 2D is static, but when you scroll through the slices you can see the change from one slice of retina (or page of a flip book) to another.  The idea is that if you follow the shape of one neuron from one 2D slice to the next, coloring each piece as you go, you can eventually discern the shape of the neuron in the 3D.  Each piece you color in the 2D builds upon the previous one.  It's like stacking blocks, each layer of blocks is flat, but as you continue stacking the blocks on top of each other you eventually get a 3D shape.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">For a less technical explanation you can view the [[http://blog.eyewire.org/behind-the-science-about-the-data/ article]] on the blog</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><references /></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><references /></div></td></tr>
</table>DannyShttps://wiki.eyewire.org/index.php?title=Serial_block-face_scanning_electron_microscopy_(SBFSEM)&diff=2533&oldid=prevDannyS at 16:04, 16 June 20142014-06-16T16:04:44Z<p></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
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<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 16:04, 16 June 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="L1" >Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Serial block-face scanning electron microscopy (SBFSEM) is a method for generating high resolution 3D images from biological samples. It was <del class="diffchange diffchange-inline">generated </del>at the Max Planck Institute in Germany, specifically for the purpose of imaging neurons.<ref name="Denk">Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure. <del class="diffchange diffchange-inline">W. Denk, H. Horstmann. http</del>:<del class="diffchange diffchange-inline">//www</del>.<del class="diffchange diffchange-inline">plosbiology.org/article/info</del>:<del class="diffchange diffchange-inline">doi/</del>10.1371/journal.pbio.0020329</ref></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Serial block-face scanning electron microscopy (SBFSEM) is a method for generating high resolution 3D images from biological samples. It was <ins class="diffchange diffchange-inline">created </ins>at the Max Planck Institute in Germany, specifically for the purpose of imaging neurons.<ref name="Denk"><ins class="diffchange diffchange-inline">Denk W, Horstmann H (2004) </ins>Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure. <ins class="diffchange diffchange-inline">PLoS Biol 2(11)</ins>: <ins class="diffchange diffchange-inline">e329</ins>. <ins class="diffchange diffchange-inline">doi</ins>:10.1371/journal.pbio.0020329</ref></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>===How EyeWire uses SBFSEM===</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>===How EyeWire uses SBFSEM===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The images you see on EyeWire come to us from our collaborators Kevin Briggman, Moritz Helmstaedter, and Winfried Denk at the Max Planck Institute in Germany. <del class="diffchange diffchange-inline"> </del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The images you see on EyeWire come to us from our collaborators Kevin Briggman, Moritz Helmstaedter, and Winfried Denk at the Max Planck Institute in Germany<ins class="diffchange diffchange-inline">, and the dataset is called [[e2198]]</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">The tissue </del>sample <del class="diffchange diffchange-inline">is first sliced using a vibratome; </del>the <del class="diffchange diffchange-inline">resulting block of tissue is then stained </del>with heavy metals <del class="diffchange diffchange-inline">(Osmium, Lead</del>, and <del class="diffchange diffchange-inline">Uranium), and then embedded in an epoxy resin (plastic)</del>. <del class="diffchange diffchange-inline">This plastic "block" is then </del>placed <del class="diffchange diffchange-inline">into a microtome</del>, <del class="diffchange diffchange-inline">where it is sliced into ultrathin slices </del>of <del class="diffchange diffchange-inline">approximately 70 microns. As each slice </del>is <del class="diffchange diffchange-inline">produced it falls into </del>a <del class="diffchange diffchange-inline">small basin </del>of <del class="diffchange diffchange-inline">water</del>, <del class="diffchange diffchange-inline">and is then picked up, sequentially, on </del>a <del class="diffchange diffchange-inline">strip of tape</del>. The <del class="diffchange diffchange-inline">tape looks much like </del>a <del class="diffchange diffchange-inline">film strip</del>, <del class="diffchange diffchange-inline">with each slice lined up </del>one <del class="diffchange diffchange-inline">after </del>the <del class="diffchange diffchange-inline">other</del>. <del class="diffchange diffchange-inline"> </del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">Before any imaging could be done, the </ins>sample <ins class="diffchange diffchange-inline">was coated with heavy metals. When </ins>the <ins class="diffchange diffchange-inline">scanning electron microscope's electrons collided </ins>with <ins class="diffchange diffchange-inline">the </ins>heavy metals <ins class="diffchange diffchange-inline">in the sample</ins>, <ins class="diffchange diffchange-inline">they would bounce off </ins>and <ins class="diffchange diffchange-inline">they would be collected by a detector</ins>. <ins class="diffchange diffchange-inline">These electrons that bounce off the sample are known as backscattered electrons. After being </ins>placed <ins class="diffchange diffchange-inline">inside the chamber of the microscope</ins>, <ins class="diffchange diffchange-inline">the surface </ins>of <ins class="diffchange diffchange-inline">the sample </ins>is <ins class="diffchange diffchange-inline">imaged. Because the Scanning Electron Microscope uses </ins>a <ins class="diffchange diffchange-inline">tightly focused beam </ins>of <ins class="diffchange diffchange-inline">electrons</ins>, <ins class="diffchange diffchange-inline">the sample needs to be scanned in </ins>a <ins class="diffchange diffchange-inline">certain pattern</ins>. The <ins class="diffchange diffchange-inline">Scanning Electron Microscope will move across </ins>a <ins class="diffchange diffchange-inline">line</ins>, <ins class="diffchange diffchange-inline">scanning it </ins>one <ins class="diffchange diffchange-inline">piece at a time, and then it will move onto </ins>the <ins class="diffchange diffchange-inline">next line. This is known as raster-scanning</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">The strip </del>of <del class="diffchange diffchange-inline">tape is cut into shorter strips</del>, <del class="diffchange diffchange-inline">and these are in turn mounted on "wafers." The wafers are then imaged using scanning electron microscopy (SEM). The SEM produces images by scanning with </del>a <del class="diffchange diffchange-inline">focused beam </del>of <del class="diffchange diffchange-inline">electrons. The electrons interact with </del>the <del class="diffchange diffchange-inline">heavy metals we stained our </del>sample <del class="diffchange diffchange-inline">with.  This produces various signals that contain information about </del>the <del class="diffchange diffchange-inline">sample’s </del>surface <del class="diffchange diffchange-inline">composition</del>. The <del class="diffchange diffchange-inline">SEM produces a huge number </del>of <del class="diffchange diffchange-inline">2D images (it images </del>each <del class="diffchange diffchange-inline">slice individually); these 2D images are then stacked on top </del>of <del class="diffchange diffchange-inline">one another </del>to form a <del class="diffchange diffchange-inline">high resolution </del>3D <del class="diffchange diffchange-inline">representation of the original tissue sample</del>.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">After the entire surface </ins>of <ins class="diffchange diffchange-inline">the sample has been imaged</ins>, a <ins class="diffchange diffchange-inline">vibratome slices off the surface </ins>of the sample <ins class="diffchange diffchange-inline">and </ins>the <ins class="diffchange diffchange-inline">underlying </ins>surface <ins class="diffchange diffchange-inline">is then imaged in the same way</ins>. The <ins class="diffchange diffchange-inline">images from the scans </ins>of each <ins class="diffchange diffchange-inline">successive layer </ins>of <ins class="diffchange diffchange-inline">the sample were combined </ins>to form a 3D <ins class="diffchange diffchange-inline">dataset</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Think of the the stack of 2D images like a [http://en.wikipedia.org/wiki/Flip_book flip book].The way flip books work is that from one page to another there is a small change in the drawing, and several small changes in a row create the action in the flip book.  The 2D image you see in EyeWire is like one single page from a flip book.  The 2D is static, but when you scroll through the slices you can see the change from one slice of retina (or page of a flip book) to another.  The idea is that if you follow the shape of one neuron from one 2D slice to the next, coloring each piece as you go, you can eventually discern the shape of the neuron in the 3D.  Each piece you color in the 2D builds upon the previous one.  It's like stacking blocks, each layer of blocks is flat, but as you continue stacking the blocks on top of each other you eventually get a 3D shape.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Think of the the stack of 2D images like a [http://en.wikipedia.org/wiki/Flip_book flip book].The way flip books work is that from one page to another there is a small change in the drawing, and several small changes in a row create the action in the flip book.  The 2D image you see in EyeWire is like one single page from a flip book.  The 2D is static, but when you scroll through the slices you can see the change from one slice of retina (or page of a flip book) to another.  The idea is that if you follow the shape of one neuron from one 2D slice to the next, coloring each piece as you go, you can eventually discern the shape of the neuron in the 3D.  Each piece you color in the 2D builds upon the previous one.  It's like stacking blocks, each layer of blocks is flat, but as you continue stacking the blocks on top of each other you eventually get a 3D shape.</div></td></tr>
</table>DannyS