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eyes:logics:angularreconstitution [2017/06/09 11:14] vzinch [Concept] |
eyes:logics:angularreconstitution [2017/06/12 18:41] (current) jschlie1 |
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| ====== AngularReconstitution ====== | ====== AngularReconstitution ====== | ||
| - | This logic determines Euler angles for a given set of input images based on the Common line theorem. This is needed in order to correctly place images (2D projections) in 3D space to get the 3D conformation of the particle | + | This logic determines Euler angles for a given set of input images based on the common line theorem. This is needed in order to correctly place images (2D projections) in 3D space prior to reconstruction. |
| ===== Usage ===== | ===== Usage ===== | ||
| - | Here, a general/generic description of HOW the logic is USED should be given. Try to be as general as possible, but also mention prerequisites, restrictions, advantages, requirements which are specific of this logic. Basically everything the user needs to know to successfully use this logic. | + | The input of this logic - class averages - should be of high quality with enough visible structural features. Choosing more class averages for this logic is not always a good idea, since similar views will result in worse angular assignment. So ideally class averages chosen should represent all possible distinct views, but without overlapping. If symmetry of the particle is known in advance, it is recommended to try running reconstitution both with and without applying symmetry restraints. Most modes of this logic only require one input (a stack of images) and generate only one output. Therefore, only divergent I/O information is mentioned below. |
| - | FIXME | + | |
| ===== Modes ===== | ===== Modes ===== | ||
| ==== Euler ==== | ==== Euler ==== | ||
| - | This mode is used for de-novo assignment of angles only from the input projections themselves | + | This mode is used for de-novo assignment of angles only from the input projections themselves. The output stack of images contains the assigned Euler angles as header values. |
| |< 100% 30% >| | |< 100% 30% >| | ||
| ^ Parameters ^ Description ^ | ^ Parameters ^ Description ^ | ||
| | Sinograms | Gives options to read already generated sinograms or to write down sinograms for the images being processed | | | Sinograms | Gives options to read already generated sinograms or to write down sinograms for the images being processed | | ||
| - | | Symmetry | Symmetry of the complex studied (if known) | | + | | Symmetry | Symmetry of the particle (if known) | |
| - | + | ||
| - | |< 100% 30% >| | + | |
| - | ^ Input ^ Description ^ | + | |
| - | | In | Image or stack of images (a set of class averages)| | + | |
| - | + | ||
| - | |< 100% 30% >| | + | |
| - | ^ Output ^ Description ^ | + | |
| - | | Out | The input projections with assigned Euler angles | | + | |
| - | + | ||
| - | FIXME | + | |
| - | + | ||
| - | |< 100% 30% >| | + | |
| - | ^ New/Changed Header Values ^ Description ^ | + | |
| - | | headerValue1 | what does it say? how is it changed? | | + | |
| - | | headerValue2 | what does it say? how is it changed? | | + | |
| - | | headerValue3 | what does it say? how is it changed? | | + | |
| - | | headerValue4 | what does it say? how is it changed? | | + | |
| ==== Anchor set ==== | ==== Anchor set ==== | ||
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| |< 100% 30% >| | |< 100% 30% >| | ||
| ^ Parameters ^ Description ^ | ^ Parameters ^ Description ^ | ||
| - | | Symmetry | Symmetry of the complex studied (if known) | | + | | Symmetry | Symmetry of the particle (if known) | |
| |< 100% 30% >| | |< 100% 30% >| | ||
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| | In | Image or stack of images (a set of class averages)| | | In | Image or stack of images (a set of class averages)| | ||
| | Anchor set | Projection set with known angular relations (mostly projected 3D-model) | | | Anchor set | Projection set with known angular relations (mostly projected 3D-model) | | ||
| - | |||
| - | |< 100% 30% >| | ||
| - | ^ Output ^ Description ^ | ||
| - | | Out | The input projections with assigned Euler angles (no anchor dataset in the output) | | ||
| - | |||
| - | |< 100% 30% >| | ||
| - | ^ New/Changed Header Values ^ Description ^ | ||
| - | | headerValue1 | what does it say? how is it changed? | | ||
| - | | headerValue2 | what does it say? how is it changed? | | ||
| - | | headerValue3 | what does it say? how is it changed? | | ||
| - | | headerValue4 | what does it say? how is it changed? | | ||
| ==== Add projection ==== | ==== Add projection ==== | ||
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| |< 100% 30% >| | |< 100% 30% >| | ||
| ^ Parameters ^ Description ^ | ^ Parameters ^ Description ^ | ||
| - | | Symmetry | Symmetry of the complex studied (if known) | | + | | Symmetry | Symmetry of the particle (if known) | |
| |< 100% 30% >| | |< 100% 30% >| | ||
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| | In | Image or stack of images (a set of class averages)| | | In | Image or stack of images (a set of class averages)| | ||
| | Dataset | Stack of images (projections) with assigned Euler angles | | | Dataset | Stack of images (projections) with assigned Euler angles | | ||
| - | |||
| - | |< 100% 30% >| | ||
| - | ^ Output ^ Description ^ | ||
| - | | Out | The input dataset with added input projections with assigned Euler angles | | ||
| - | |||
| - | |< 100% 30% >| | ||
| - | ^ New/Changed Header Values ^ Description ^ | ||
| - | | headerValue1 | what does it say? how is it changed? | | ||
| - | | headerValue2 | what does it say? how is it changed? | | ||
| - | | headerValue3 | what does it say? how is it changed? | | ||
| - | | headerValue4 | what does it say? how is it changed? | | ||
| ==== Sinograms ==== | ==== Sinograms ==== | ||
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| |< 100% 30% >| | |< 100% 30% >| | ||
| ^ Parameters ^ Description ^ | ^ Parameters ^ Description ^ | ||
| - | | Symmetry | Symmetry of the complex studied (if known) | | + | | Symmetry | Symmetry of the particle (if known) | |
| - | |< 100% 30% >| | ||
| - | ^ Input ^ Description ^ | ||
| - | | In | Image or stack of images | | ||
| - | |||
| - | |< 100% 30% >| | ||
| - | ^ Output ^ Description ^ | ||
| - | | Out | Sinogram | | ||
| - | |||
| - | |< 100% 30% >| | ||
| - | ^ New/Changed Header Values ^ Description ^ | ||
| - | | headerValue1 | what does it say? how is it changed? | | ||
| - | | headerValue2 | what does it say? how is it changed? | | ||
| - | | headerValue3 | what does it say? how is it changed? | | ||
| - | | headerValue4 | what does it say? how is it changed? | | ||
| ===== Concept ===== | ===== Concept ===== | ||
| - | + | This logic is needed as an intermediate step to get from 2D images to a 3D volume. In order to reconstruct the full volume we need to know the relationship between the images (projections) we have - how they are located in 3D relative to each other. | |
| - | This logic is needed as an intermediate step to get 3D model from 2D images. In order to reconstruct the full model we need to know the relationship between the images (projections) we have - how they are located in 3D relative to each other. | + | |
| In case any reference model for the particle is available, it can be used as 'anchor set' that would increase the precision of the output. | In case any reference model for the particle is available, it can be used as 'anchor set' that would increase the precision of the output. | ||
| - | However, when no prior model is available for the particles of interest, determination of [[https://en.wikipedia.org/wiki/Euler_angles|Euler angles]] should be done de novo. This logic does it based on [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334316|Common line theorem]]. | + | However, when no prior model is available for the particles of interest, determination of [[https://en.wikipedia.org/wiki/Euler_angles|Euler angles]] should be done de novo. This logic does it based on [[http://www.sciencedirect.com/science/article/pii/0304399187900787|Common line theorem]]. |