Programmatic GUI customization for template matching - Revision history

Raffaele Coray: /* Testing chunk autocorrelation from GUI */

2025-02-13T14:58:52Z

Testing chunk autocorrelation from GUI

Raffaele Coray: /* Getting the data */

2024-12-03T12:32:57Z

Getting the data

Raffaele Coray: /* Acknowledgements */

2024-11-29T15:18:18Z

Acknowledgements

Raffaele Coray at 15:16, 29 November 2024

2024-11-29T15:16:09Z

Raffaele Coray at 15:07, 29 November 2024

2024-11-29T15:07:36Z

Raffaele Coray: /* Getting the data */

2024-11-29T15:05:43Z

Getting the data

Raffaele Coray: /* Testing chunk autocorrelation from GUI */

2024-11-29T15:05:00Z

Testing chunk autocorrelation from GUI

Raffaele Coray: /* Testing chunk autocorrelation from GUI */

2024-11-29T15:04:41Z

Testing chunk autocorrelation from GUI

Raffaele Coray: /* Testing chunk autocorrelation from GUI */

2024-11-29T15:03:58Z

Testing chunk autocorrelation from GUI

Raffaele Coray: /* Testing chunk autocorrelation from GUI */

2024-11-29T15:03:33Z

Testing chunk autocorrelation from GUI

@@ Line 187: / Line 187: @@
 # <tt>tm.addMenuGlobal('Plot tessellation with cone orientations',myFunction,'Separator','On','Accelerator','Q');</tt> makes so that a new Template Matching menu options will be created that generates an event causing the function to be executed.<br>
-=== Testing chunk autocorrelation from GUI ===
+=== Testing new functionality from GUI ===
 Click on the "Template Matching" option on the top bar of the GUI. The new functionality button will appear as in the following figure.
 [[ File:GUI_with_added_general_functionality.png |thumb|center|500px| Newly added functionality.]]

@@ 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, a fourier mask fmaskMCP.mrc and a tessellation file tesselation3.omd.

@@ 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 [[Walkthrough on command line 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.
+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.
 == Adding per-chunk functionality ==

← Older revision		Revision as of 15:16, 29 November 2024
Line 28:		Line 28:
	=== Acknowledgements ===		=== 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 command line 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.
−

@@ Line 6: / Line 6: @@
 It is through this tab that general attributes of chunks distributions and TM processes can be manipulated.
 Additionally, each chunk has its own attributes (such as position and size) that can be manipulated after they are created.
-More information on how to use the GUI can be found in LINKLINKLINK.
+More information on how to use the GUI can be found in [[Walkthrough for GUI-based template matching | the GUI walkthrough]].
 == Programmatic addition of GUI functionalities ==

@@ Line 111: / Line 111: @@
 [[ File:GUI_with_added_chunk_functionality.png |thumb|center|500px| Newly added functionality.]]
-Click the button and inspect the resulting auto-correlation map. After ensuring better contrast, the resulting map will appear as the following image.
+Click the button and inspect the resulting auto-correlation map. After ensuring better contrast, the resulting map will appear as the following image, highlighting the MCP array.
 [[ File:auto_correlation_map_of_top_chunk.png |thumb|center|500px| Auto-correlation of chunk.]]