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eyes:logics:ctfcorrection [2017/06/12 16:03] kbertra2 created |
eyes:logics:ctfcorrection [2017/06/12 18:33] (current) jschlie1 |
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| - | ====== Ctf Correction ====== | + | ====== CTFCorrection ====== |
| - | This logic can estimate ctf parameters for class sums, apply previously calculated ones to images and also lets the user choose the parameters manually. This correction for the phase information modulation during the imaging process is an essential part of getting high resolution structures out of input data. | + | This logic can estimate ctf parameters from particle power spectra class sums, apply previously calculated ones to images and also lets the user choose the parameters manually. This correction for the phase information modulation during the imaging process is an essential part of getting high resolution structures out of input data. |
| ===== Usage ===== | ===== Usage ===== | ||
| - | If Ctf parameters are to be estimated, the user needs to provide class sums due to the higher signal-to-noise ratio as compared to images. Afterwards, the images that make up the class sums can be corrected through the determined parameters, as well as images that contain the ctf information in their header. | + | If Ctf parameters are to be estimated, the user needs to provide class sums of classified power spectra due to the higher signal-to-noise ratio as compared to images. Afterwards, the images that make up the class sums can be corrected through the determined parameters, as well as images that contain the ctf information in their header. |
| ===== Example ==== | ===== Example ==== | ||
| - | Here, a very specific example should be given/described. In the future, this can be supported by screenshots etc.. For the moment, give an example easy enough for the user to understand, but specific enough to elaborate why a given parameter is a good set for this very situation. | + | To push one's dataset to the limits, estimating and applying ctf parameters is needed. So the user would classify the power spectra of the dataset's particles and then estimate the ctf parameters from the resulting classsums. The parameters from this (or from ctf correction of micrographs) can then either be applied directly or, as they're stored as header values, used in successive refinement. |
| ===== Modes/Processes ===== | ===== Modes/Processes ===== | ||
| - | ==== thisIsTheNameOfMode1 ==== | ||
| - | Here, a short introduction for the given mode should be placed. Again, state WHAT and WHY this mode us useful in not more than 2 sentences. | ||
| + | ==== Compute CTF parameters ==== | ||
| + | |||
| + | In this mode, ctf parameters are calculated from input power spectra class sums through comparison with theoretical power spectra. | ||
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| ^ Parameters ^ Description ^ | ^ Parameters ^ Description ^ | ||
| - | | Some changeable parameter | Description of this parameter | | + | | Spherical Abberration | The spherical abberration of the microscope | |
| - | | -> and its sub-parameter | more description | | + | | Max astigmatism | The spherical abberration of the microscope | |
| - | | Next main parameter | and more more more | | + | | Max defocus | Maximum defocus to be considered for the first estimation round | |
| - | | -> and its sub-parameter | ... descriptions | | + | | Min defocus | Minimum defocus to be considered for the first estimation round | |
| + | | High tension in kV | Acceleration voltage of the microscope | | ||
| + | | Pixel size of class sum power spectra | Power spectra's pixel size | | ||
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| ^ Input ^ Description ^ | ^ Input ^ Description ^ | ||
| - | | FirstInput | Input Description 1 | | + | | Input Images| Power spectra class sums. Each sum needs to have "classId" in the header | |
| - | | SecondInput | Input Description 2 | | + | |
| - | | //ThirdInput// | Input Description 3: Optional Input in Italic | | + | |
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| ^ Output ^ Description ^ | ^ Output ^ Description ^ | ||
| - | | FirstOutput | Output Description | | + | | Classes with ctf info| The input images with ctf information in the header| |
| + | | Half-half PS| Half input image, half fitted power spectrum to show validity of the fit| | ||
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| ^ New/Changed Header Values ^ Description ^ | ^ New/Changed Header Values ^ Description ^ | ||
| - | | headerValue1 | what does it say? how is it changed? | | + | |classId| The class id of the power spectrum| |
| - | | headerValue2 | what does it say? how is it changed? | | + | |defocus| The estimated defocus| |
| - | | headerValue3 | what does it say? how is it changed? | | + | |bFactor| The estimated b-factor| |
| - | | headerValue4 | what does it say? how is it changed? | | + | |bFactorExp| The estimated b-factor exponent| |
| + | |astigmMag| The estimated magnitude of the astigmatism| | ||
| + | |astigmDir| The direction of the astigmatism| | ||
| + | |amplitudeContrastRatio| The ratio of amplitude to phase contrast| | ||
| + | |qualityOfPSFit|The cross-correlation coefficient of the power spectrum of the class and the theoretical estimated power spectrum| | ||
| + | |accelerationVoltage|The acceleration voltage used during image acquisition| | ||
| + | |pixelSize| The pixel size of the image| | ||
| + | |sphericalAberration| The spherical aberration of the image| | ||
| - | ==== thisIsTheNameOfMode2 ==== | + | ==== Impose CTF parameters on images ==== |
| - | Here, a short introduction for the given mode should be placed. Again, state WHAT and WHY this mode us useful in not more than 2 sentences. | + | In this mode, ctf parameters are applied on input images.They can be provided from the power spectra class sums, out of image headers or through manual input |
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| ^ Parameters ^ Description ^ | ^ Parameters ^ Description ^ | ||
| - | | Some changeable parameter | Description of this parameter | | + | | Value location: Get from class sums | Specifies that the power spectra class sums that were used for estimation will be provided as a value source| |
| - | | -> and its sub-parameter | more description | | + | | -> Limit based rejection of values | Enables rejection of unrealistic values through comparison with micrograph fit values. For this to work, cropCenterX and cropCenterY need to be in the header | |
| - | | Next main parameter | and more more more | | + | | -> -> Pixel size of origin micrographs | The pixel size of the images that micrograph ctf correction was performed on | |
| - | | -> and its sub-parameter | ... descriptions | | + | | -> -> Sidelength of micrographs | Sidelength of the original micrographs(for now, only square ones are supported| |
| + | | Value location: Provided in image headers | Reads the parameters from the header files | | ||
| + | | -> Group identifier | The header key that specifies which images share the same parameters so that they can be corrected together | | ||
| + | | Value location: Manual user input | Applies parameters that are specified by the user. This is recommended for testing only | | ||
| + | | -> Astigmatism angle in degrees | Astigmatism angle to be applied| | ||
| + | | -> DefocusU | DefocusU to be applied| | ||
| + | | -> DefocusV | DefocusV to be applied| | ||
| + | | -> High tension| DefocusV to be applied| | ||
| + | | -> Spherical abberation(Cs)| Spherical aberation to be applied| | ||
| + | |||
| + | | Apply softfilter mask | Whether to apply a mask with a soft edge onto the input images | | ||
| + | | Desired size of corrected output images | The size that the corrected images should have | | ||
| + | | Pixel size in Angstrom | Pixel size that the images have | | ||
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| ^ Input ^ Description ^ | ^ Input ^ Description ^ | ||
| - | | FirstInput | Input Description 1 | | + | | Particles | The images to be corrected | |
| - | | SecondImput | Input Description 2 | | + | | Value location: Get from class sums | |
| - | | ThridImput | Input Description 1 | | + | | -> Half-half PS (or classes with ctf info) | The half-half PS output from previous correction | |
| + | | -> Particle power spectra | Power spectra of the particles | | ||
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| - | ^ Output ^ Description ^ | ||
| - | | FirstOutput | Output Description | | ||
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| - | ^ New/Changed Header Values ^ Description ^ | + | ^ Output ^ Description ^ |
| - | | headerValue1 | what does it say? how is it changed? | | + | | Corrected images| The images with flipped phases | |
| - | | headerValue2 | what does it say? how is it changed? | | + | | Amplitude masks| Amplitude masks that were used for correction| |
| - | | headerValue3 | what does it say? how is it changed? | | + | | Uncorrected images| Basically the same images as were put into the logic| |
| - | | headerValue4 | what does it say? how is it changed? | | + | |
| ===== Concept ===== | ===== Concept ===== | ||
| - | In this paragraph, the "HOW a logic works under the hood" and WHY someone should use it can be elaborated with higher detail. Describes a scenario in an image processing workflow where this logic can be used to solve the resulting problem. Also, wikipages, publications or anything else describing the theory behind an algorithm should be linked here, if applicable. | + | This method of ctf correction is based on a paper from the stark lab [[http://www.sciencedirect.com/science/article/pii/S1047847703000728|paper from the stark lab ]] |