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eyes:logics:optimizereferences [2017/06/08 15:29] vzinch [Concept] |
eyes:logics:optimizereferences [2017/06/12 18:36] (current) jschlie1 |
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| ====== OptimizeReferences ====== | ====== OptimizeReferences ====== | ||
| - | This logic aligns the class averages so that they are in the same direction. | + | This logic aligns class averages so that they share the same mutual orientation. |
| - | After classification step different classes might contain the same view, but rotated in the image plane, so alignment is needed for the same views to look identical. | + | After a classification step different classes might contain the same view, but rotated in the image plane (i.e. different α-angles), so an alignment is needed to optimize the class averages before using them as references for image alignment. |
| ===== Usage ===== | ===== Usage ===== | ||
| The quality of the output heavily depends on the quality of the first class average chosen - preferably, it should show enough details of the molecule or complex and be surrounded by a black rim. | The quality of the output heavily depends on the quality of the first class average chosen - preferably, it should show enough details of the molecule or complex and be surrounded by a black rim. | ||
| - | The optimal values suggested for radius parameter are around 0.8-0.9. | + | The optimal values suggested for radius parameter are around 0.8-0.9. |
| - | + | ===== Parameters ===== | |
| - | ===== Example ===== | + | |
| - | FIXME | + | |
| - | + | ||
| - | ===== Process ===== | + | |
| |< 100% 30% >| | |< 100% 30% >| | ||
| ^ Parameters ^ Description ^ | ^ Parameters ^ Description ^ | ||
| | Correlation Function | The correlation function that is optimized during the image alignment | | | Correlation Function | The correlation function that is optimized during the image alignment | | ||
| - | | Fraction | The maximal fraction of the image that will be shifted relative to reference image during the alignment | | + | | Fraction | The maximal fraction of the image that will be shifted relative to the reference image during the alignment | |
| | Interpolation | Defines the interpolation function used to get the value between two neighbouring pixels | | | Interpolation | Defines the interpolation function used to get the value between two neighbouring pixels | | ||
| | Radius | The value of Circular Mask Fraction (this fraction of image dimension will be used as diameter of the circle cut from the image for cf calculations)| | | Radius | The value of Circular Mask Fraction (this fraction of image dimension will be used as diameter of the circle cut from the image for cf calculations)| | ||
| | Sampling | The maximal fraction of the image shifted during the alignment relative to the reference image | | | Sampling | The maximal fraction of the image shifted during the alignment relative to the reference image | | ||
| - | |||
| - | |< 100% 30% >| | ||
| - | ^ Input ^ Description ^ | ||
| - | | Input | A set of class averages | | ||
| - | |||
| - | |< 100% 30% >| | ||
| - | ^ Output ^ Description ^ | ||
| - | | Output | A set of aligned class averages | | ||
| - | |||
| - | |< 100% 30% >| | ||
| - | ^ Written Header Values ^ Description ^ | ||
| - | | resolutionAt0.143 | Estimated resolution for FSC cut off at 0.143 | | ||
| - | | resolutionAt0.3 | Estimated resolution for FSC cut off at 0.3 | | ||
| - | | resolutionAt0.5 | Estimated resolution for FSC cut off at 0.5 | | ||
| - | | resolutionAt0.9 | Estimated resolution for FSC cut off at 0.9 | | ||
| - | | resolutionAt3Sigma | Estimated resolution for FSC cut off at 3 Sigma | | ||
| - | | resolution | Estimated resolution at the user chosen cut off value | | ||
| - | | maxResolution | Maximum resolution in the local map | | ||
| - | | meanResolution | Mean resolution in the local map | | ||
| - | | minResolution | Minimum resolution in the local map | | ||
| - | | resolutionVariance | Variance of the resolution in the local map | | ||
| - | | abscissaIsLogarithmical , abscissaMin, abscissaMax | For internal 1D viewer use only, to be hidden | | ||
| - | FIXME | ||
| ===== Concept ===== | ===== Concept ===== | ||
| The logic takes a stack of class average images as input. It applies the circular mask of radius changed by parameter 'Radius' to every image, so that only the defined circle and not the surrounding noise will be used for correlation calculations. Then the logic aligns every image to the first one by shifting them in [[https://en.wikipedia.org/wiki/Polar_coordinate_system|polar coordinates]] (that corresponds to rotation of image in Cartesian coordinates) and maximizing the correlation function. | The logic takes a stack of class average images as input. It applies the circular mask of radius changed by parameter 'Radius' to every image, so that only the defined circle and not the surrounding noise will be used for correlation calculations. Then the logic aligns every image to the first one by shifting them in [[https://en.wikipedia.org/wiki/Polar_coordinate_system|polar coordinates]] (that corresponds to rotation of image in Cartesian coordinates) and maximizing the correlation function. | ||