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eyes:logics:ctfcorrection [2017/06/12 17:10] lschult |
eyes:logics:ctfcorrection [2017/06/12 18:33] (current) jschlie1 |
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| - | ====== Ctf Correction ====== | + | ====== CTFCorrection ====== |
| 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. | 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. | ||
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| ==== Impose CTF parameters on images ==== | ==== Impose CTF parameters on images ==== | ||
| + | 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 | ||
| |< 100% 30% >| | |< 100% 30% >| | ||
| ^ 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 | | ||
| |< 100% 30% >| | |< 100% 30% >| | ||
| ^ Input ^ Description ^ | ^ Input ^ Description ^ | ||
| - | | FirstInput | Input Description 1 | | + | | Particles | The images to be corrected | |
| - | | SecondInput | Input Description 2 | | + | | Value location: Get from class sums | |
| - | | //ThirdInput// | Input Description 3: Optional Input in Italic | | + | | -> Half-half PS (or classes with ctf info) | The half-half PS output from previous correction | |
| + | | -> Particle power spectra | Power spectra of the particles | | ||
| |< 100% 30% >| | |< 100% 30% >| | ||
| ^ Output ^ Description ^ | ^ Output ^ Description ^ | ||
| - | | FirstOutput | Output Description | | + | | Corrected images| The images with flipped phases | |
| + | | Amplitude masks| Amplitude masks that were used for correction| | ||
| + | | Uncorrected images| Basically the same images as were put into the logic| | ||
| - | |< 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 ===== | ||
| - | 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 ]] |