Walkthrough for GUI-based template matching - Revision history

Raffaele Coray: /* Getting the data */

2024-12-03T12:34:19Z

Getting the data

Raffaele Coray: /* Manipulation a tessellation with the GUI */

2024-11-29T15:26:18Z

Manipulation a tessellation with the GUI

Raffaele Coray: /* Run model-aware TM with manual tesselation */

2024-11-29T15:23:38Z

Run model-aware TM with manual tesselation

Raffaele Coray: /* Run model-aware TM with manual tesselation */

2024-11-29T15:23:16Z

Run model-aware TM with manual tesselation

Raffaele Coray: /* Relationship between GUI models and tessellations */

2024-11-29T15:22:03Z

Relationship between GUI models and tessellations

Raffaele Coray: /* Relationship between GUI models and tesselations */

2024-11-29T15:21:30Z

Relationship between GUI models and tesselations

Raffaele Coray: /* Relationship between GUI models and tesselations */

2024-11-29T15:20:59Z

Relationship between GUI models and tesselations

Raffaele Coray: /* Acknowledgements */

2024-11-29T15:19:04Z

Acknowledgements

Raffaele Coray: /* Template matching */

2024-11-29T15:09:44Z

Template matching

Raffaele Coray: /* Getting the data */

2024-11-29T15:06:01Z

Getting the data

@@ Line 18: / Line 18: @@
 Currently the data necessary to tun this walkthrough can be downloaded using the link:
-https://drive.google.com/file/d/1ME2r6cDw6_sJVtFPTFTgOVBWIuQn44Wl/view?usp=drive_link
+<!--https://drive.google.com/file/d/1ME2r6cDw6_sJVtFPTFTgOVBWIuQn44Wl/view?usp=drive_link-->
 It consists in: a tomogram fullReconstructionWBPCTFDW.mrc, a template templateMCP.mrc, a mask maskMCP.mrc and a fourier mask fmaskMCP.mrc.

← Older revision		Revision as of 15:26, 29 November 2024
Line 286:		Line 286:
	<tt>dpktomo.match.modelling.setUpTilingTable</tt>		<tt>dpktomo.match.modelling.setUpTilingTable</tt>

−	More information on this can be found in the tutorial.~~XXXXXXXXXXXXXXXXXXXX~~	+	More information on this can be found in the tutorial [[Walkthrough for model-aware template matching \| on model-aware template matching]].
		+
		+
		+	=== Programmatic GUI customization for template matching ===
		+
		+	It is possible to add custom functionalities to the GUI as described in the [[Programmatic GUI customization for template matching \| corresponding tutorial]].

@@ Line 240: / Line 240: @@
 </pre>
-=== Run model-aware TM with manual tesselation ===
+=== Run model-aware TM with manual tessellation ===
 Finally, a full model-aware TM process can be run.

@@ Line 247: / Line 247: @@
   'ytilt',[-60,60],'is',10,'cs',10,'bin',2,'mw',10,'gpus',1,'tilingTable',star);</tt>
-The resulting TM object pts_GPU can be then used as in the tutorials XXXXX and YYYYYYY.
+The resulting TM object pts_GPU can be then used as in the tutorials [[Walkthrough for template matching | on basic TM]] and [[Walkthrough for model-aware template matching | model-aware TM]].
 == Additional functionalities ==

@@ Line 144: / Line 144: @@
 == Relationship between GUI models and tessellations ==
-The GUI allows the creation and manipulation of tessellation with the tool mentioned in the previous section. However, these tessaltion will be save or loaded from .omd files. This can be done from the "Template Matching" tab in the GUI with the options "Save chunk distribution" and "Load chunk distribution from .omd file".<br>
+The GUI allows the creation and manipulation of tessellation with the tool mentioned in the previous section. However, these tessellations will be saved or loaded from .omd files. This can be done from the "Template Matching" tab in the GUI with the options "Save chunk distribution" and "Load chunk distribution from .omd file".<br>
 However, TM processes require a tessellation in either table or dStar format as described in the tutorial [[Walkthrough for model-aware template matching | on model-aware template matching]]. This difference in format exists because .omd file tessellations are simplified so that their representations in the GUI would not be cumbersome. As such two converting functions are available in the Dynamo TM package:

@@ Line 142: / Line 142: @@
 It should be noted that the area of the chunk that will generate valid cross-correlation scores is reduced by half of the size of the template in all directions.
-== Relationship between GUI models and tesselations ==
+== Relationship between GUI models and tessellations ==
-The GUI allows the creation and manipulation of tesselation with the tool mentioned in the previous section. However, these tessaltion will be save or loaded from .omd files. This can be done from the "Template Matching" tab in the GUI with the options "Save chunk distribution" and "Load chunk distribution from .omd file".<br>
+The GUI allows the creation and manipulation of tessellation with the tool mentioned in the previous section. However, these tessaltion will be save or loaded from .omd files. This can be done from the "Template Matching" tab in the GUI with the options "Save chunk distribution" and "Load chunk distribution from .omd file".<br>
-However, TM processes require a tessellation in either table or dStar format as described in the tutorial [[Walkthrough for model-aware template matching | on model-aware template matching]]. This difference in format exists because .omd file tesselations are simplified so that their representations in the GUI would not be cumbersome. As such two converting functions are available in the Dynamo TM package:
+However, TM processes require a tessellation in either table or dStar format as described in the tutorial [[Walkthrough for model-aware template matching | on model-aware template matching]]. This difference in format exists because .omd file tessellations are simplified so that their representations in the GUI would not be cumbersome. As such two converting functions are available in the Dynamo TM package:
-The function <tt>dpktomo.match.modelling.createTesselationFromGUIomd</tt> converts an .omd tesselation into a dStar tesselation ready for <tt>dynamo_match</tt>.<br>
+The function <tt>dpktomo.match.modelling.createTesselationFromGUIomd</tt> converts an .omd tessellation into a dStar tessellation ready for <tt>dynamo_match</tt>.<br>
-The function <tt>dpktomo.match.modelling.saveTesselationAsGUIomd</tt> converts a dStar tesselation into an object that can be saved as a .omd file with <tt>dwrite</tt>.<br>
+The function <tt>dpktomo.match.modelling.saveTesselationAsGUIomd</tt> converts a dStar tessellation into an object that can be saved as a .omd file with <tt>dwrite</tt>.<br>
 == Walkthrough on chunk manipulation ==

@@ Line 28: / Line 28: @@
 === Acknowledgements ===
-The tomogram has been generated using the tilt series from EMPIAR dataset entry 10226 described in the paper "Chreifi, G., Chen, S., Metskas, L. A., Kaplan, M., & Jensen, G. J. (2019b). Rapid tilt-series acquisition for electron cryotomography. Journal of Structural Biology, 205(2), 163–169. https://doi.org/10.1016/j.jsb.2018.12.008". The alignment and reconstruction was done using the Dynamo AWF procedureLINKLINK as detailed in "Coray, R., Navarro, P., Scaramuzza, S., Stahlberg, H., & Castaño-Díez, D. (2024). Automated fiducial-based alignment of cryo-electron tomography tilt series in Dynamo. Structure, 32(10), 1808-1819.e4. https://doi.org/10.1016/j.str.2024.07.003". The template has been generated by STA as described in the same paper.
+The tomogram has been generated using the tilt series from EMPIAR dataset entry 10226 described in the paper "Chreifi, G., Chen, S., Metskas, L. A., Kaplan, M., & Jensen, G. J. (2019b). Rapid tilt-series acquisition for electron cryotomography. Journal of Structural Biology, 205(2), 163–169. https://doi.org/10.1016/j.jsb.2018.12.008". The alignment and reconstruction was done using the [[Walkthrough on GUI based tilt series alignment | Dynamo AWF procedure]] as detailed in "Coray, R., Navarro, P., Scaramuzza, S., Stahlberg, H., & Castaño-Díez, D. (2024). Automated fiducial-based alignment of cryo-electron tomography tilt series in Dynamo. Structure, 32(10), 1808-1819.e4. https://doi.org/10.1016/j.str.2024.07.003". The template has been generated by STA as described in the same paper.
 === Visualizing the tomogram ===

@@ Line 10: / Line 10: @@
 In this walkthrough, the methods to manually manipulate these chunk is introduced.
-Walkthroughs on basic TM in Dynamo and model-aware TM are also available LINKLINK.
+Walkthroughs on [[Walkthrough for template matching | basic TM]] in Dynamo and [[Walkthrough for model-aware template matching | model-aware TM]] are also available.
 == Data set ==