Fourier compensation during averaging - Revision history

Daniel Castaño: /* Use bigger boxes */

2017-11-21T10:06:22Z

Use bigger boxes

Daniel Castaño at 14:52, 15 April 2016

2016-04-15T14:52:08Z

Daniel Castaño at 14:50, 15 April 2016

2016-04-15T14:50:10Z

Daniel Castaño at 08:51, 14 April 2016

2016-04-14T08:51:16Z

Daniel Castaño at 08:50, 14 April 2016

2016-04-14T08:50:41Z

Daniel Castaño at 08:49, 14 April 2016

2016-04-14T08:49:36Z

Daniel Castaño: Created page with "{{Category: processing steps}} During averaging, all the particles that pass the threshold are aligned (rotated and translated) and added together. Rotating a particle in di..."

2016-04-14T08:37:12Z

Created page with "{{Category: processing steps}} During averaging, all the particles that pass the threshold are aligned (rotated and translated) and added together. Rotating a particle in di..."

New page

{{Category: processing steps}}

During averaging, all the particles that pass the threshold are aligned (rotated and translated) and added together.

Rotating a particle in direct space implies rotating its Fourier transform, which has a [[Fourier sampling|missing wedge]]. Even if all the particles may come from a single tomogram and thus share the same missing wedge, after rotation each particle will cover a different area of the Fourier space. As the particles have different orientations, any voxel in the Fourier Space will have a different number of particles contributing to it. Any Fourier component will be non-zero for some particles and zero (representing missing information) for others.

As each particle has a different missing wedge, the resulting addition is not "well compensated", meaning that some Fourier components are more represented than others. In order to compute the average, each computed Fourier component has to be divided with the actual number of particles that have contributed to it.

Thus, the result of adding the aligned particles together without any special step for fourier compensation is called ''raw average''. A raw average has to be compensated.

The way ''Dynamo''performs the Fourier compensation is by keeping track of the number of times a rotated particle contributes to a Fourier component. While computing the raw average, each missing wedge is rotated and added into a volume. This volume has the size of a particle if Fourier space. It is called an {{t|fweight}} in ''Dynamo''jargon (a Fourier weight) and represents the number of particles that contributed to each Fourier Component.

Then the 'compensated average''(called simply {{t|average}} inside a project) gets computed by dividing the raw average in fourier space with the computed fweight. The used function is {{t|dynamo_fweight_divide}}

== Artifacts from strongly inhomogeneous information quality

== Artifacts from particle rotation ==

===Smoothing mask===
It is possible to tell Dynamo to impose an smoothing mask (in direct space) onto the raw average before dividing it in fourier space with the fweight.

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 ===Use bigger boxes===
-T.B.I. A [[dadata folder]] can include for each particle entry a ''container'' entry that represents the same particle cropped with a bigger sidelength. During execution of the project, the small particle will be used for alignment (to save time), and the ''container'' particles will be used for averaging (to ensure exact removal of rotation artifacts during fourier compensation)
+T.B.I. A [[data folder]] can include for each particle entry a ''container'' entry that represents the same particle cropped with a bigger sidelength. During execution of the project, the small particle will be used for alignment (to save time), and the ''container'' particles will be used for averaging (to ensure exact removal of rotation artifacts during fourier compensation)
 ===Crop directly from tomogram===

@@ Line 22: / Line 22: @@
 == Artifacts  from particle rotation ==
-While rotating a cube, there is always  [[rotation edge | rotation artifact]]
+While rotating a cube, there is always  a [[ Border alignment artifact | rotation artifact]]
 ===Use bigger boxes===

← Older revision		Revision as of 14:50, 15 April 2016
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	== Artifacts from strongly inhomogeneous information quality ==		== Artifacts from strongly inhomogeneous information quality ==

		+	They might happen when individual Fourier components contributed by few particles are surrounded by components contributed by many particles. The latest are less noisy that the former ones. Even if the compensation (in terms of division with the exact number of contributing particles) is exact, the disbalance in noise content can create an instability.

		+	This can be solved stating a valui for the 'fmin' parameter, which states the minimum number of contributions that a Fourier component needs to have in order to be accepted.

	== Artifacts from particle rotation ==		== Artifacts from particle rotation ==

@@ Line 30: / Line 30: @@
 ===Smoothing mask===
-It is possible to tell Dynamo to impose an smoothing mask (in direct space) onto the raw average before dividing it in fourier space with the {{t|fweight}.
+It is possible to tell Dynamo to impose an smoothing mask (in direct space) onto the raw average before dividing it in fourier space with the {{t|fweight}}.
 The user can:
 * pass the parameters for on-the-fly construction of a smoothing mask
 * pass the name of a file.
 * use the smoothing mask used in FSC computations also for this task.

← Older revision		Revision as of 08:50, 14 April 2016
Line 11:		Line 11:
	The way ''Dynamo''performs the Fourier compensation is by keeping track of the number of times a rotated particle contributes to a Fourier component. While computing the raw average, each missing wedge is rotated and added into a volume. This volume has the size of a particle if Fourier space. It is called an {{t\|fweight}} in ''Dynamo''jargon (a Fourier weight) and represents the number of particles that contributed to each Fourier Component.		The way ''Dynamo''performs the Fourier compensation is by keeping track of the number of times a rotated particle contributes to a Fourier component. While computing the raw average, each missing wedge is rotated and added into a volume. This volume has the size of a particle if Fourier space. It is called an {{t\|fweight}} in ''Dynamo''jargon (a Fourier weight) and represents the number of particles that contributed to each Fourier Component.

−	Then the 'compensated average''(called simply {{t\|average}} inside a project) gets computed by dividing the raw average in fourier space with the computed fweight. The used function is {{t\|dynamo_fweight_divide}}	+	Then the ''compensated average'' (called simply {{t\|average}} inside a project) gets computed by dividing the raw average in fourier space with the computed fweight. The used function is {{t\|dynamo_fweight_divide}}

@@ Line 1: / Line 1: @@
-{{Category: processing steps}}
+{{Category: generic steps}}
 During averaging, all the particles that pass the threshold are aligned (rotated and translated) and added together.
@@ Line 14: / Line 14: @@
-== Artifacts from strongly inhomogeneous information quality
+== Artifacts from strongly inhomogeneous information quality ==
 == Artifacts  from particle rotation ==
 ===Smoothing mask===
-It is possible to tell Dynamo to impose an smoothing mask (in direct space) onto the raw average before dividing it in fourier space with the fweight.
+It is possible to tell Dynamo to impose an smoothing mask (in direct space) onto the raw average before dividing it in fourier space with the {{t|fweight}.