Walkthrough on manual marker clicking - Revision history

Raffaele Coray: /* Loading the data */

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← Older revision		Revision as of 14:20, 3 December 2024
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	[[File:ManualAlignmentDmarkers.png\|thumb\|center\|600px\| <tt>dmarkers</tt> GUI ]]-->		[[File:ManualAlignmentDmarkers.png\|thumb\|center\|600px\| <tt>dmarkers</tt> GUI ]]-->
−	~~[[File:ManualAlignmentDmarkers.png\|thumb\|center\|600px\| <tt>dmarkers</tt> GUI ]]~~

	== Basic visualization controls ==		== Basic visualization controls ==

← Older revision		Revision as of 14:20, 3 December 2024
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	[[File:ManualAlignmentDmarkers.png\|thumb\|center\|600px\| <tt>dmarkers</tt> GUI ]]-->		[[File:ManualAlignmentDmarkers.png\|thumb\|center\|600px\| <tt>dmarkers</tt> GUI ]]-->
		+	[[File:ManualAlignmentDmarkers.png\|thumb\|center\|600px\| <tt>dmarkers</tt> GUI ]]

	== Basic visualization controls ==		== Basic visualization controls ==

← Older revision		Revision as of 14:19, 3 December 2024
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	here, <tt>gui</tt> is just a handle to the GUI. This handle can be used on a later point to operate on it. Note that we also need to pass the tilt angles, as they will be needed for fitting a projection model.		here, <tt>gui</tt> is just a handle to the GUI. This handle can be used on a later point to operate on it. Note that we also need to pass the tilt angles, as they will be needed for fitting a projection model.

−	[[File:~~alignGUI_openTomoshowOnTheFullSizedMatrixToCheckTheSizeOfAGoldBead~~.png\|thumb\|center\|600px\| <tt>dmarkers</tt> GUI ]]	+	[[File:manual_marker_HIV_TS.png\|thumb\|center\|600px\| <tt>dmarkers</tt> GUI ]]

@@ Line 6: / Line 6: @@
 We use a binned version of the first tilt series from the EMPIAR entry 10164, depicting a set of virus like particles (VLP). You can download it directly from EMPIAR, then bin it,   <!--[https://drive.google.com/file/d/1EsnKBvbFuWD1njk8dRVLc3SlhdsTHIpY/view?usp=drive_link or simply follow this link]-->[{{Template:DownloadLinkAWFHIV1TS}} or simply follow this link] to download a 600Mb file. You can also follow this tutorial using your own data.
-<!--This tutorial uses the tilt series VPP_tomo4.mrc from the EMPIAR database entry 10064. You can download it directly from the website: <!--https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10064/-->{{Template:DownloadLinkAWFmanualEMPIAR}}
+<!--This tutorial uses the tilt series VPP_tomo4.mrc from the EMPIAR database entry 10064. You can download it directly from the website: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10064/{{Template:DownloadLinkAWFmanualEMPIAR}}
 The tilt series has already been prepared and can be found by following the next steps.-->

@@ Line 4: / Line 4: @@
 = Data set =
-This tutorial uses the tilt series VPP_tomo4.mrc from the EMPIAR database entry 10064. You can download it directly from the website: <!--https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10064/-->{{Template:DownloadLinkAWFmanualEMPIAR}}
+<!--This tutorial uses the tilt series VPP_tomo4.mrc from the EMPIAR database entry 10064. You can download it directly from the website: <!--https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10064/-->{{Template:DownloadLinkAWFmanualEMPIAR}}
-The tilt series has already been prepared and can be found by following the next steps.
+The tilt series has already been prepared and can be found by following the next steps.-->
 Note that this tilt series has the following tilt angles: <code>-57:3:60</code>.

@@ Line 20: / Line 20: @@
 It is convenient to first read the tilt series: <br/>
   <tt>ts = dread('b001ts001.mrc');</tt>
 and then pass the variable to the gui <tt>dmarkers</tt>:

← Older revision		Revision as of 14:14, 3 December 2024
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	here, <tt>gui</tt> is just a handle to the GUI. This handle can be used on a later point to operate on it. Note that we also need to pass the tilt angles, as they will be needed for fitting a projection model.		here, <tt>gui</tt> is just a handle to the GUI. This handle can be used on a later point to operate on it. Note that we also need to pass the tilt angles, as they will be needed for fitting a projection model.

−	[[File:~~ManualAlignmentDmarkers~~.png\|thumb\|center\|600px\| <tt>dmarkers</tt> GUI ]]	+	[[File:alignGUI_openTomoshowOnTheFullSizedMatrixToCheckTheSizeOfAGoldBead.png\|thumb\|center\|600px\| <tt>dmarkers</tt> GUI ]]

@@ Line 16: / Line 16: @@
 == Loading the data ==
 Opening the <tt>dmarkers</tt> GUI on a tilt series:
@@ Line 34: / Line 33: @@
 [[File:ManualAlignmentDmarkers.png|thumb|center|600px| <tt>dmarkers</tt> GUI ]]
 == Basic visualization controls ==

← Older revision		Revision as of 12:44, 2 December 2024
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		+	[[Category:Walkthroughs]]
		+
	This walkthrough describes the tools to ''manually'' locate fiducial markers for tilt series alignment using different graphical tools. ''Automatic'' alignment is described in [[Walkthrough on GUI based tilt series alignment]] and [[Walkthrough on command line based tilt series alignment ]].		This walkthrough describes the tools to ''manually'' locate fiducial markers for tilt series alignment using different graphical tools. ''Automatic'' alignment is described in [[Walkthrough on GUI based tilt series alignment]] and [[Walkthrough on command line based tilt series alignment ]].