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eyes:logics:optimizereferences [2017/06/12 15:20] vzinch [Process] |
eyes:logics:optimizereferences [2017/06/12 18:36] (current) jschlie1 |
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| ===== 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 ===== | |
| - | + | ||
| - | ===== Process ===== | + | |
| |< 100% 30% >| | |< 100% 30% >| | ||
| ^ Parameters ^ Description ^ | ^ Parameters ^ Description ^ | ||
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| | 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 | | ||
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| ===== 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. | ||