Many thanks for your suggestion.
I am adding one HTML exported page below, which contains both a TOC as well as Sub Pages list. Both were not removed by the script.
In addition, most of the attachment were not converted properly by Pandoc and I had to fix them with a sed command.
Eyal
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EMU wiki : Copy of SPA SerialEM-K3 protocol updated 20-Jul-22 (v4.1)
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Created by <span class='author'> Eyal Shimoni</span>, last modified on Sep 18, 2022
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<p><br/></p><p><span><span><span><span>Table of contents<br/></span></span></span></span></p><p><style type='text/css'>/*<![CDATA[*/
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<li><a href='#CopyofSPASerialEM-K3protocolupdated20-Jul-22(v4.1)-Importantnotes,pleaseread'>Important notes, please read</a></li>
<li><a href='#CopyofSPASerialEM-K3protocolupdated20-Jul-22(v4.1)-Microscopeandcamerasetups'>Microscope and camera setups</a></li>
<li><a href='#CopyofSPASerialEM-K3protocolupdated20-Jul-22(v4.1)-Sampleloading'>Sample loading</a></li>
<li><a href='#CopyofSPASerialEM-K3protocolupdated20-Jul-22(v4.1)-StartSerialEMandmakegridmap'>Start SerialEM and make grid map</a></li>
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<p>Sub Pages</p><p class="auto-cursor-target"><ul class='childpages-macro'><li><a href="Test-page-1_31293902.html">Test page 1</a><ul class='childpages-macro'><li><a href="Test-page-2_31293905.html">Test page 2</a></li><li><a href="Test-page-2b_31293911.html">Test page 2b</a></li></ul></li><li><a href="Test-page-3_31293908.html">Test page 3</a></li><li><a href="Test-page-4_31293913.html">Test page 4</a></li></ul></p></div>
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<div class="confluence-information-macro confluence-information-macro-information"><span class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span><div class="confluence-information-macro-body"><h3 id="CopyofSPASerialEM-K3protocolupdated20-Jul-22(v4.1)-Help">Help</h3></div></div></div>
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<p><span class="confluence-anchor-link" id="CopyofSPASerialEM-K3protocolupdated20-Jul-22(v4.1)-important_notes"></span></p><div class="confluence-information-macro confluence-information-macro-warning"><span class="aui-icon aui-icon-small aui-iconfont-error confluence-information-macro-icon"></span><div class="confluence-information-macro-body"><h1 id="CopyofSPASerialEM-K3protocolupdated20-Jul-22(v4.1)-Importantnotes,pleaseread">Important notes, please read</h1><h3 id="CopyofSPASerialEM-K3protocolupdated20-Jul-22(v4.1)-Backupanddiscspace">Backup and disc space</h3><ul><li style="list-style-type: none;background-image: none;"><ol><li><p><span style="color: rgb(0,0,0);">Make sure you have enough free space on the <strong>Gatan computer X drive</strong>. The disc has 10T in total and it fills up very quickly.</span></p></li><li><p><span style="color: rgb(0,0,0);">Backup your data during the session using datasync or copy it immediately after the session as explained <a href="https://iblcnfappv01.weizmann.ac.il/display/EW/Data+transfer+and+temporary+backup"><span>here</span></a>. Data left on the microscope disc can be deleted anytime.</span></p></li><li><span style="color: rgb(0,0,0);"><span style="color: rgb(0,0,0);">Please save all data, including <span>Grid maps</span> to a folder with your name and date directly under X.</span></span></li></ol></li></ul><h3 id="CopyofSPASerialEM-K3protocolupdated20-Jul-22(v4.1)-Monitoryoursession">Monitor your session</h3><ol><li><span style="color: rgb(0,0,0);"><span style="color: rgb(0,0,0);">The automated run may be interrupted from various reasons. It is therefore highly recommended to <span style="color: rgb(0,0,0);">frequently </span>check that the session is running fine.</span></span><span style="color: rgb(0,0,0);"><span style="color: rgb(0,0,0);"><br/></span></span></li></ol><h3 id="CopyofSPASerialEM-K3protocolupdated20-Jul-22(v4.1)-K3andgainreference"><span style="color: rgb(0,0,0);">K3 and gain reference</span></h3><ol><li><span style="color: rgb(0,0,0);"><span style="color: rgb(0,0,0);">The K3 requires a new <strong>dark reference</strong> every few hours. This is automated in EPU and SeriaEM. See below how to take a new dark reference in GMS. One indication of the need for a new dark reference is when a horizontal thick bright line appears in the middle of the images.</span></span></li></ol><h3 id="CopyofSPASerialEM-K3protocolupdated20-Jul-22(v4.1)-Gridhandling">Grid handling</h3><ol><li><span style="color: rgb(0,0,0);">Please remove your grids from the Autoloader <span style="color: rgb(0,0,0);">at the end of your session</span></span></li></ol></div></div><p><br/></p></div>
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<h1 id="CopyofSPASerialEM-K3protocolupdated20-Jul-22(v4.1)-Microscopeandcamerasetups"><span style="color: rgb(0,0,0);">Microscope and camera setups</span></h1><ol><li><span style="color: rgb(0,0,0);">On microscope computer:</span><ol><li><span style="color: rgb(0,0,0);">Usually software are running, if not open the following: TEM User Interface, FluCam Viewer, TIA.</span></li><li><span style="color: rgb(0,0,0);"><strong>Check that microscope is cold</strong>: Autoloader tab > Temperature control> in cryo the temperatures will be around -185C<br/></span></li><li><span style="color: rgb(0,0,0);">FEG and HT are on, vacuum is OK (Setup tab)</span></li><li><span style="color: rgb(0,0,0);">Tomography software and EPU are off</span></li><li><span style="color: rgb(0,0,0);">Autoloader turbo is off: Autoloader tab > Autoloader > flapout > Make sure 'Turbo Auto Off' is clicked</span></li><li><span style="color: rgb(0,0,0);">K3 is identified: Camera tab > CCD/TV Camera > Camera: EF-CCD</span></li></ol></li><li><span style="color: rgb(0,0,0);">Load and check microscope alignment:</span><ol><li><span style="color: rgb(0,0,0);">Load the <strong>column alignment</strong> (the most updated one: <strong>APM_D3775HT300</strong>)</span><ol><li><span style="color: rgb(0,0,0);">Alignment tab > Alignments > flap out > File tab > click on a file > select all entries under "Available" and click left arrow to add to "Selected" > Apply</span></li></ol></li><li><p><span style="color: rgb(0,0,0);">Load your <strong>FEG register</strong></span></p><ol><li><span style="color: rgb(0,0,0);">Open your FEG register file: </span><br/><ol><li><span style="color: rgb(0,0,0);">Setup tab > FEG registers > flap out > File tab > Open > select your file</span></li><li><span style="color: rgb(0,0,0);">The directory for your personal FEG register file is: E:\User_DATA\groupFolder<br/></span></li></ol></li><li><span style="color: rgb(0,0,0);">Set the FEG register for <strong>imaging</strong>:</span><br/><ol><li><span style="color: rgb(0,0,0);">Setup tab > FEG registers > select one register > Set<br/></span></li></ol></li></ol></li><li><span style="color: rgb(0,0,0);">Check beam alignment:</span><br/><ol><li><span style="color: rgb(0,0,0);">Open column valve, lower screen</span></li><li><span style="color: rgb(0,0,0);">In the FluCam set the "GIF" mark only. The green circle marks the entrance aperture of the energy filter. Centering of the beam is done to this circle. </span></li><li><span style="color: rgb(0,0,0);">Press Normalize all (L1), wait until stabilizes</span></li><li><span style="color: rgb(0,0,0);">Press Eucentric Focus, wait until stabilizes</span></li><li><span style="color: rgb(0,0,0);">Look at the beam. The beam should be aligned or almost aligned.</span></li><li><span style="color: rgb(0,0,0);">Tune tab > Direct alignments > adjust Beam Shift if needed.</span></li></ol></li></ol></li><li><span style="color: rgb(0,0,0);">Gatan computer:</span><ol><li><span style="color: rgb(0,0,0);">Open GMS3 and make sure you are in Power User mode: Help > User Mode > Power User</span></li><li><span style="color: rgb(0,0,0);">Check energy filter (GIF) alignment: </span><br/><ol><li><span style="color: rgb(0,0,0);">Lift the screen</span></li><li><span style="color: rgb(0,0,0);">In GMS (Gatan computer): </span><br/><ol><li><span style="color: rgb(0,0,0);">EF-CCD Camera panel > choose 1x > start the View > This will insert the camera (takes ~30 sec). Clicking again on View will stop the live imaging.</span></li><li><span style="color: rgb(0,0,0);">Check that the image is not distorted or partially blocked (usually at the right). If the image is blocked or distorted try to load another GIF alignment file: Filter control window > Open file (icon at the bottom, no need to save the current one) > Open default GIB setting file</span></li></ol></li></ol></li><li><span style="color: rgb(0,0,0);">If the Gatan PC was restarted: Desktop> right-click GfiRemote, GCiRemote & GatanRPCServer Launcher icons and for each of these shortcuts > Run with PowerShell</span></li></ol></li></ol></div>
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<div class="confluence-information-macro confluence-information-macro-information"><span class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span><div class="confluence-information-macro-body"><p>The Krios is usually very stable, so by loading the column alignment + FEG register, the microscope state that you saved in the previous session will be restored. Only minor alignments are usually needed.</p><p><span style="color: rgb(0,51,102);"><strong>Column alignments: </strong><br/></span></p><ul><li><span style="color: rgb(255,0,0);"><span style="color: rgb(255,0,0);"><span style="color: rgb(0,51,102);">Managed by the staff.</span><br/></span></span></li><li><span style="color: rgb(0,0,0);">There are several column alignments files, for different purposes. </span></li></ul><p><span style="color: rgb(0,0,0);"><strong>FEG registers</strong>: <br/></span></p><ul><li><span style="color: rgb(0,0,0);">Managed by the users</span></li><li><span style="color: rgb(0,0,0);">Contain adjustments on top of the column alignment file including direct alignments, microscope state, astigmatism correction, apertures, gun lens, spot size and more. </span></li><li><span style="color: rgb(0,0,0);">It recommended to <strong>update and save</strong> your FEG register after you adjustment them: </span><br/>Setup tab > FEG registers > choose the one to update > click "Update" > flap out > File tab > Save.<br/>To add a new FEG register: Type a new name name at the bottom of the module > click "Add" > flap out > File tab > Save.</li><li><span style="color: rgb(0,0,0);">In this protocol FEG registers should <span><span>set the microscope to <span style="color: rgb(0,0,0);"><span><span><strong>EFTEM</strong></span></span></span> <strong>nP </strong>(= Energey Filterred TEM + nano probe)</span></span>.</span></li><li><span style="color: rgb(0,0,0);"><strong>It is convenient, but not essential</strong>, to have 3 different FEG registers in your file. These function as shortcuts for quickly moving between microscope states:</span><ol><li><strong>Imaging</strong> - with settings for data acquisition. Direct alignments and counting gain reference are done on this FEG register.</li><li><strong>Tune GIF</strong> - high dose for tuning the energy filter,<span style="color: rgb(0,0,0);"> same magnification as for imaging.</span></li><li><strong>Linear gain reference</strong> - the dose needed for doing the Linear gain reference, wide beam.</li></ol></li></ul></div></div></div>
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<p><br/></p><hr/><h1 id="CopyofSPASerialEM-K3protocolupdated20-Jul-22(v4.1)-Sampleloading">Sample loading</h1></div>
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<ol><li><span style="color: rgb(0,0,0);">Go load your samples.</span></li><li><span style="color: rgb(0,0,0);">Make sure the orientation of the grid is favorable for acquiring tilt series of lamella. There should be a notch marked on the rim of the clip ring. This notch should face the side (parallel to the table surface) when you load it into the cassette. If you load it facing you, you can afterwards rotate the stage 90 degrees to get the lamellae aligned with the tilt axis.</span></li><li><span style="color: rgb(0,0,0);">After cassette insertion wait until the temperature is below -170°C everywhere in autoloader.</span></li><li><span style="color: rgb(0,0,0);"> Autoloader tab > flap-out > click "Inventory"</span></li><li><span style="color: rgb(0,0,0);">Insert grid to column: Autoloader tab > press on one of the positions > press "Load". Wait until slot turns yellow.</span></li></ol></div>
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<p><br/></p><div class="confluence-information-macro confluence-information-macro-warning"><span class="aui-icon aui-icon-small aui-iconfont-error confluence-information-macro-icon"></span><div class="confluence-information-macro-body"><p>If the inventory indicates an empty slot where there should be a loaded grid, do not continue with the protocol and call a staff member.</p><p>Recommended to look at the video at - <a href="https://em-learning.com/" class="external-link" rel="nofollow">https://em-learning.com/</a> see "Sample preparation” sections 4 and 5. Also at <a href="https://www.youtube.com/playlist?list=PL8_xPU5epJdfd5fM2CjQItR-iRlIEIJk8" class="external-link" rel="nofollow">https://www.youtube.com/playlist?list=PL8_xPU5epJdfd5fM2CjQItR-iRlIEIJk8</a></p></div></div><p><br/></p></div>
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<p><span class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img class="confluence-embedded-image" height="400" src="attachments/31293879/31293882.png" data-image-src="attachments/31293879/31293882.png" data-unresolved-comment-count="0" data-linked-resource-id="31293882" data-linked-resource-version="1" data-linked-resource-type="attachment" data-linked-resource-default-alias="autoloader-annotated.PNG" data-base-url="https://iblcnfappv01.weizmann.ac.il" data-linked-resource-content-type="image/png" data-linked-resource-container-id="31293879" data-linked-resource-container-version="5"></span></p></div>
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<p><br/></p><hr/><h1 id="CopyofSPASerialEM-K3protocolupdated20-Jul-22(v4.1)-StartSerialEMandmakegridmap">Start SerialEM and make grid map</h1></div>
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<ol><li><span style="color: rgb(0,0,0);">Start SerialEM server on microscope computer (star icon on taskbar)</span></li><li><span style="color: rgb(0,0,0);">Start SerialEM from your shortcut: Gatan desktop > SerialEM Shortcuts folder</span></li><li><span style="color: rgb(0,0,0);">Load your SerialEM setting: Settings menu > Open... . The folder for Settings files is: C:\ProgramData\SerialEM\UserSettings\Your_Group_Folder. <strong>Do not save data in this folder</strong><br/></span></li><li><span style="color: rgb(0,0,0);">Navigator menu > Open</span></li><li><span style="color: rgb(0,0,0);">Navigator > Open Imaging states (if necessary)</span></li><li><span style="color: rgb(0,0,0);">Imaging States > Grid map (82x) > click Imaging</span></li><li><span style="color: rgb(0,0,0);">Look in FluCam, make sure you can see the grid and that beam is centered.</span></li><li><span style="color: rgb(0,0,0);">Using GMS view mode, manually roughly correct eucentric height.</span></li><li><span style="color: rgb(0,0,0);">Navigator menu > Montage & Grids > </span><br/><ol><li><span style="color: rgb(0,0,0);">Setup Full Montage > Parameters: mag 82x, Bin 1, X: 4 Y: 6, Min Overlap 15% and 0.5 micron, Move stage instead of shifting image, Ask about making map, Use Montage Mapping > OK ></span></li><li><span style="color: rgb(0,0,0);">OK in "File properties" (default options) ></span></li><li><span style="color: rgb(0,0,0);">Save map file to a folder X:\DoseFractions\date_yourName_maps\<br/></span></li></ol></li><li><span style="color: rgb(0,0,0);">Montage control panel > Start </span><br/><ol><li><span style="color: rgb(0,0,0);">Parameters in montage control panel: Show overview, Align pieces in overview</span></li></ol></li><li><span style="color: rgb(0,0,0);">This will run the montage. When it finishes > click Yes to make map from montage.</span></li><li><span style="color: rgb(0,0,0);">Move map to new window: Window > New window</span></li><li><span style="color: rgb(0,0,0);">Save the Navigator: Navigator menu > Save</span></li><li><span style="color: rgb(0,0,0);">Close the map file: File menu > Close</span></li></ol></div>
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<div class="confluence-information-macro confluence-information-macro-information"><span class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span><div class="confluence-information-macro-body"><ul><li><span style="color: rgb(0,0,0);">Mont-map mode should have "single image", binning 1, exposure time 0.25 sec, full area.</span> Adjusted in the Camera Setup dialog</li></ul></div></div></div>
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<div class="cell aside" data-type="aside">
<div class="innerCell">
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<div class="columnLayout single" data-layout="single">
<div class="cell normal" data-type="normal">
<div class="innerCell">
<p><br/></p></div>
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</div>
<div class="columnLayout single" data-layout="single">
<div class="cell normal" data-type="normal">
<div class="innerCell">
<p><br/></p></div>
</div>
</div>
<div class="columnLayout single" data-layout="single">
<div class="cell normal" data-type="normal">
<div class="innerCell">
<p><br/></p></div>
</div>
</div>
<div class="columnLayout two-right-sidebar" data-layout="two-right-sidebar">
<div class="cell normal" data-type="normal">
<div class="innerCell">
<p><br/></p></div>
</div>
<div class="cell aside" data-type="aside">
<div class="innerCell">
<p><br/></p></div>
</div>
</div>
<div class="columnLayout single" data-layout="single">
<div class="cell normal" data-type="normal">
<div class="innerCell">
<p><br/></p></div>
</div>
</div>
<div class="columnLayout two-right-sidebar" data-layout="two-right-sidebar">
<div class="cell normal" data-type="normal">
<div class="innerCell">
<p><br/></p></div>
</div>
<div class="cell aside" data-type="aside">
<div class="innerCell">
<p><br/></p></div>
</div>
</div>
<div class="columnLayout single" data-layout="single">
<div class="cell normal" data-type="normal">
<div class="innerCell">
<p><br/></p></div>
</div>
</div>
<div class="columnLayout single" data-layout="single">
<div class="cell normal" data-type="normal">
<div class="innerCell">
<p><br/></p></div>
</div>
</div>
<div class="columnLayout single" data-layout="single">
<div class="cell normal" data-type="normal">
<div class="innerCell">
<p><br/></p></div>
</div>
</div>
<div class="columnLayout two-equal" data-layout="two-equal">
<div class="cell normal" data-type="normal">
<div class="innerCell">
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</div>
<div class="cell normal" data-type="normal">
<div class="innerCell">
<p><br/></p></div>
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<div class="columnLayout single" data-layout="single">
<div class="cell normal" data-type="normal">
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<div class="columnLayout single" data-layout="single">
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<div class="pageSection group">
<div class="pageSectionHeader">
<h2 id="attachments" class="pageSectionTitle">Attachments:</h2>
</div>
<div class="greybox" align="left">
<img src="images/icons/bullet_blue.gif" height="8" width="8" alt=""/>
<a href="attachments/31293879/31293880.jpg">AcquireAtItems_Square_Data.JPG</a> (image/jpeg)
<br/>
<img src="images/icons/bullet_blue.gif" height="8" width="8" alt=""/>
<a href="attachments/31293879/31293881.jpg">AcquireAtItems_Square_maps.JPG</a> (image/jpeg)
<br/>
<img src="images/icons/bullet_blue.gif" height="8" width="8" alt=""/>
<a href="attachments/31293879/31293882.png">autoloader-annotated.PNG</a> (image/png)
<br/>
<img src="images/icons/bullet_blue.gif" height="8" width="8" alt=""/>
<a href="attachments/31293879/31293883.jpg">grid_map_montage_control.JPG</a> (image/jpeg)
<br/>
<img src="images/icons/bullet_blue.gif" height="8" width="8" alt=""/>
<a href="attachments/31293879/31293884.jpg">grid_map_montage_setup_file_properties.JPG</a> (image/jpeg)
<br/>
<img src="images/icons/bullet_blue.gif" height="8" width="8" alt=""/>
<a href="attachments/31293879/31293885.jpg">grid_map_mont-map_camera_setup.JPG</a> (image/jpeg)
<br/>
<img src="images/icons/bullet_blue.gif" height="8" width="8" alt=""/>
<a href="attachments/31293879/31293886.jpg">hole_finder.JPG</a> (image/jpeg)
<br/>
<img src="images/icons/bullet_blue.gif" height="8" width="8" alt=""/>
<a href="attachments/31293879/31293887.jpg">measure_distance_between_holes.JPG</a> (image/jpeg)
<br/>
<img src="images/icons/bullet_blue.gif" height="8" width="8" alt=""/>
<a href="attachments/31293879/31293888.jpg">square_map_montage_setup.JPG</a> (image/jpeg)
<br/>
<img src="images/icons/bullet_blue.gif" height="8" width="8" alt=""/>
<a href="attachments/31293879/31293889.jpg">square_maps_acqure_at_points.JPG</a> (image/jpeg)
<br/>
<img src="images/icons/bullet_blue.gif" height="8" width="8" alt=""/>
<a href="attachments/31293879/31293890.jpg">file_properties_for_montage_setup.JPG</a> (image/jpeg)
<br/>
<img src="images/icons/bullet_blue.gif" height="8" width="8" alt=""/>
<a href="attachments/31293879/31293891.jpg">Grid_map_montage_setup.JPG</a> (image/jpeg)
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<p>Document generated by Confluence on Sep 18, 2022 12:12</p>
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