Tilt angle convention - Revision history

Daniel Castaño: /* Cheat sheet */

2020-06-10T11:42:37Z

Cheat sheet

Daniel Castaño: /* Cheat sheet */

2020-06-10T11:41:55Z

Cheat sheet

Daniel Castaño: /* Cheat sheet */

2020-06-10T11:40:04Z

Cheat sheet

Daniel Castaño: /* Cheat sheet */

2020-06-10T08:43:53Z

Cheat sheet

Daniel Castaño: /* Cheat sheet */

2020-06-10T08:31:46Z

Cheat sheet

Daniel Castaño at 08:28, 10 June 2020

2020-06-10T08:28:37Z

Stefano Scaramuzza at 16:28, 5 April 2019

2019-04-05T16:28:43Z

Stefano Scaramuzza at 16:42, 1 February 2019

2019-02-01T16:42:34Z

Stefano Scaramuzza at 14:23, 31 January 2019

2019-01-31T14:23:01Z

Stefano Scaramuzza at 10:06, 30 January 2019

2019-01-30T10:06:45Z

@@ Line 14: / Line 14: @@
 * For negative tilt angles, the left side of the images should be more underfocused than the right side.
 * A positive tilt angle means that the stage has been tilted by  that  angle ''clockwise'' about the ''positive'' ''y'' direction.
-* Thus, higher heights in the tomogram are more underfocused (i.e., have larger defocus values).
+* Higher heights in the untilted sample are more underfocused (i.e., have larger defocus values).
 For visual reference, check Figure 1 in [https://reader.elsevier.com/reader/sd/pii/S1047847717301272?token=8E810667E3A42758016F23FA22A4C948318CB5698DA54E24EECEAF234754D8ED9262F1B595440D0309C15DD33EF26808 Journal of Structural Biology 199 (2017) 187–195.]. Dynamo follows the convention depicted there.

← Older revision		Revision as of 11:41, 10 June 2020
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	* Thus, higher heights in the tomogram are more underfocused (i.e., have larger defocus values).		* Thus, higher heights in the tomogram are more underfocused (i.e., have larger defocus values).

−	For visual reference, check Figure ~~2 of~~ [https://reader.elsevier.com/reader/sd/pii/S1047847717301272?token=8E810667E3A42758016F23FA22A4C948318CB5698DA54E24EECEAF234754D8ED9262F1B595440D0309C15DD33EF26808 Journal of Structural Biology 199 (2017) 187–195.]	+	For visual reference, check Figure 1 in [https://reader.elsevier.com/reader/sd/pii/S1047847717301272?token=8E810667E3A42758016F23FA22A4C948318CB5698DA54E24EECEAF234754D8ED9262F1B595440D0309C15DD33EF26808 Journal of Structural Biology 199 (2017) 187–195.]. Dynamo follows the convention depicted there.

@@ Line 14: / Line 14: @@
 * For negative tilt angles, the left side of the images should be more underfocused than the right side.
 * A positive tilt angle means that the stage has been tilted by  that  angle ''clockwise'' about the ''positive'' ''y'' direction.
-* Thus, higher heights in the tomogram are more underfocused (i.e., have larger defocus values)
+* Thus, higher heights in the tomogram are more underfocused (i.e., have larger defocus values).

@@ Line 13: / Line 13: @@
 * By convention, "underfocus" entails positive defocus values.
 * For negative tilt angles, the left side of the images should be more underfocused than the right side.
-* A positive tilt angle means that the stage has been tilted by  that  angle ''clockwise''.
+* A positive tilt angle means that the stage has been tilted by  that  angle ''clockwise'' about the ''positive'' ''y'' direction.
 * Thus, higher heights in the tomogram are more underfocused (i.e., have larger defocus values)

@@ Line 12: / Line 12: @@
 = Cheat sheet =
 * By convention, "underfocus" entails positive defocus values.
-* For negative tilt angles,  the left side of the images should be more underfocused than the right side
+* For negative tilt angles, the left side of the images should be more underfocused than the right side.
-*  A positive tilt angle means that the stage has been tilted that  angle ''clockwise''
+* A positive tilt angle means that the stage has been tilted by  that  angle ''clockwise''.
 * Thus, higher heights in the tomogram are more underfocused (i.e., have larger defocus values)

← Older revision		Revision as of 08:28, 10 June 2020
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	If this is not the case, the angles in the tilt file have to be adapted accordingly. To be completely certain, after correcting the signs of the angles, a rearrangement of the images in the stack can be made so that the first tilt image has the angle of -60 degrees. Alternatively, instead of changing the tilt angle file, the tilt image stack itself can be rotated by 180 degrees. In both cases, be aware of what processing steps were already made with the wrong convention and if some of them need to be repeated with the correct angle convention. After having applied the corrections, plot again the defocus to double check that everything has worked well.		If this is not the case, the angles in the tilt file have to be adapted accordingly. To be completely certain, after correcting the signs of the angles, a rearrangement of the images in the stack can be made so that the first tilt image has the angle of -60 degrees. Alternatively, instead of changing the tilt angle file, the tilt image stack itself can be rotated by 180 degrees. In both cases, be aware of what processing steps were already made with the wrong convention and if some of them need to be repeated with the correct angle convention. After having applied the corrections, plot again the defocus to double check that everything has worked well.
		+
		+	= Cheat sheet =
		+	* By convention, "underfocus" entails positive defocus values.
		+	* For negative tilt angles, the left side of the images should be more underfocused than the right side
		+	* A positive tilt angle means that the stage has been tilted that angle ''clockwise''
		+	* Thus, higher heights in the tomogram are more underfocused (i.e., have larger defocus values)

← Older revision		Revision as of 16:28, 5 April 2019
Line 2:		Line 2:
	Dynamo, [https://bio3d.colorado.edu/imod/ IMOD] and [https://github.com/turonova/novaCTF/wiki novaCTF], by default, all use the same convention for the sign of the tilt angle of an image within a tilt series: At positive tilt angles, the right side of the tilt images is expected to be more underfocused than the left side. It is important that the tilt angles of your corresponding tilt series follow this convention. This ensures that within these different software packages the true handedness of the tomogram is not lost, the CTF corrections are done properly and missing wedge masks for incomplete tilt series are applied correctly.		Dynamo, [https://bio3d.colorado.edu/imod/ IMOD] and [https://github.com/turonova/novaCTF/wiki novaCTF], by default, all use the same convention for the sign of the tilt angle of an image within a tilt series: At positive tilt angles, the right side of the tilt images is expected to be more underfocused than the left side. It is important that the tilt angles of your corresponding tilt series follow this convention. This ensures that within these different software packages the true handedness of the tomogram is not lost, the CTF corrections are done properly and missing wedge masks for incomplete tilt series are applied correctly.

−	To test if the angles in your tilt series follow the convention, the defocus on the left and right side of the tilt series can be estimated and plotted against the angles of the corresponding tilt angle file. It is recommended to use the aligned tilt series for this estimation because there the tilt axis goes vertical through the center and it will also not change its orientation anymore in later processing steps. The result should look more or less like the following figure:	+	To test if the angles in your tilt series follow the convention, the defocus on the left and right side of the tilt series can be estimated and plotted against the angles of the corresponding tilt angle file. It is recommended to use the aligned tilt series for this estimation because there the tilt axis goes vertical through the center and it will also not change its orientation anymore in later processing steps. The result should look more or less like the following figure. An example function to generate this plot can be found in [https://github.com/C-CINA/TomographyTools TomographyTools].

← Older revision		Revision as of 16:42, 1 February 2019
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−	If this is not the case, the angles in the tilt file have to be adapted accordingly. To be completely certain, after correcting the signs of the angles, a rearrangement of the images in the stack can be made so that the first tilt image has the angle of -60 degrees.	+	If this is not the case, the angles in the tilt file have to be adapted accordingly. To be completely certain, after correcting the signs of the angles, a rearrangement of the images in the stack can be made so that the first tilt image has the angle of -60 degrees. Alternatively, instead of changing the tilt angle file, the tilt image stack itself can be rotated by 180 degrees. In both cases, be aware of what processing steps were already made with the wrong convention and if some of them need to be repeated with the correct angle convention. After having applied the corrections, plot again the defocus to double check that everything has worked well.

@@ Line 1: / Line 1: @@
 [[Category:Conventions]]
-Dynamo, [https://bio3d.colorado.edu/imod/ IMOD] and [https://github.com/turonova/novaCTF/wiki novaCTF], by default, all use the same convention for the sign of the tilt angle of an image within a tilt series: At positive tilt angles, the right side of the tilt images is expected to be more underfocused than the left side. It is important to ensure that the tilt angles of your corresponding tilt series follow this convention. You do this to make sure that within those software packages the true handedness of the tomogram is not lost, the CTF corrections are done properly and missing wedge masks for incomplete tilt series are applied correctly.
+Dynamo, [https://bio3d.colorado.edu/imod/ IMOD] and [https://github.com/turonova/novaCTF/wiki novaCTF], by default, all use the same convention for the sign of the tilt angle of an image within a tilt series: At positive tilt angles, the right side of the tilt images is expected to be more underfocused than the left side. It is important that the tilt angles of your corresponding tilt series follow this convention. This ensures that within these different software packages the true handedness of the tomogram is not lost, the CTF corrections are done properly and missing wedge masks for incomplete tilt series are applied correctly.
-To test if the convention is respected in your tilt series, the defocus on the left and right side of the tilt series can be estimated and plotted against the angles of the corresponding tilt angle file. It is recommended to use the aligned tilt series for this estimation because there the tilt axis goes vertical through the center and it will also not change its orientation anymore in later processing steps. The result should look more or less like this:
+To test if the angles in your tilt series follow the convention, the defocus on the left and right side of the tilt series can be estimated and plotted against the angles of the corresponding tilt angle file. It is recommended to use the aligned tilt series for this estimation because there the tilt axis goes vertical through the center and it will also not change its orientation anymore in later processing steps. The result should look more or less like the following figure:

@@ Line 1: / Line 1: @@
 [[Category:Conventions]]
-Dynamo, [https://bio3d.colorado.edu/imod/ IMOD] and [https://github.com/turonova/novaCTF/wiki novaCTF], by default, all use the same convention for the sign of the tilt angle of an image within a tilt series: At positive tilt angles, the right side of the tilt images is expected to be more underfocused than the left side. It is important to ensure that the tilt angles of the corresponding tilt series follow this convention. This is to make sure that within those software packages the true handedness of the tomogram is not lost, the CTF corrections are done properly and missing wedge masks for incomplete tilt series are applied correctly.
+Dynamo, [https://bio3d.colorado.edu/imod/ IMOD] and [https://github.com/turonova/novaCTF/wiki novaCTF], by default, all use the same convention for the sign of the tilt angle of an image within a tilt series: At positive tilt angles, the right side of the tilt images is expected to be more underfocused than the left side. It is important to ensure that the tilt angles of your corresponding tilt series follow this convention. You do this to make sure that within those software packages the true handedness of the tomogram is not lost, the CTF corrections are done properly and missing wedge masks for incomplete tilt series are applied correctly.
-To test if the convention is respected in your tilt series, the defocus on the left and right side of the tilt series can be estimated and plotted against the angles of the corresponding tilt angle file. It is recommended to use the aligned tilt series for this estimation. The result should look more or less like this:
+To test if the convention is respected in your tilt series, the defocus on the left and right side of the tilt series can be estimated and plotted against the angles of the corresponding tilt angle file. It is recommended to use the aligned tilt series for this estimation because there the tilt axis goes vertical through the center and it will also not change its orientation anymore in later processing steps. The result should look more or less like this:
-  [[File:defocus_left_right.png|thumb|center|400px| Plot of estimated defocus from full micrographs of a tilt series (blue), only left side of micrographs (red) and only right side of micrographs (yellow). If for the tilts 1-20 the left side has a higher defocus, the angles for these tilts should be negative. Analogously, the tilts 22-41 should have a positive angle if the right side has a higher defocus.]]
+  [[File:defocus_left_right.png|thumb|center|400px| Plot of estimated defocus from full micrographs of a tilt series (blue), only left side of micrographs (red) and only right side of micrographs (yellow). If for the tilts 1-20 the left side has a higher defocus, the angles for these tilts should be ''negative''. Analogously, the tilts 22-41 should have a ''positive'' angle if the right side has a higher defocus.]]
 If this is not the case, the angles in the tilt file have to be adapted accordingly. To be completely certain, after correcting the signs of the angles, a rearrangement of the images in the stack can be made so that the first tilt image has the angle of -60 degrees.