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eyes:logics:sharpen3d [2017/06/08 09:59] nfische |
eyes:logics:sharpen3d [2017/06/13 15:17] (current) lschult |
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| - | ======Sharpen 3D ====== | + | ======Sharpen3D ====== |
| - | THIS position should be used for a brief introduction (max 2 sentences!) of the logic, stating WHAT and WHY it is doing something. | + | Map sharpening allows to correct for the contrast loss at high resolution, resulting in better interpretable maps. |
| + | =====Usage===== | ||
| + | Use this module to sharpen and subsequently low-pass filter a 3d map. Sharpening helps in interpreting the map: dependent on resolution of the map domains, secondary structure elements or side-chains will be more clearly defined. Sharpening can be either performed using a standard curve from SAXS data((Gabashvili, I.S., et al. (2001). Solution Structure of the E. coli 70S Ribosome at 11.5 Å Resolution. Cell, 100(5), 537-49.)) | ||
| + | ("Do not use custom experimental data"; generally more conservative) or using a reference curve from a custom 3d volume ("Use custom experimental data"), e.g. a theoretical density computed from an atomic model. In the latter case, the pixel size of the reference must be provided. Sharpening also increases the high-resolution noise, which may impede reliable interpretation, in particular in less-well resolved regions of the map. Consequently, homogeneously well-resolved maps may subsequently be filtered in global mode, i.e. every part of the map is low-pass filtered to the same resolution. Heterogeneously resolved maps may be be filtered in local mode, i.e. individual regions are filtered according to the respective local resolution. | ||
| - | ===== 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. | ||
| - | ===== Example ==== | + | ===== Process ===== |
| - | 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. | + | |
| - | + | ||
| - | ===== 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. | + | |
| - | + | ||
| - | |< 100% 30% >| | + | |
| - | ^ Parameters ^ Description ^ | + | |
| - | | Some changeable parameter | Description of this parameter | | + | |
| - | | -> and its sub-parameter | more description | | + | |
| - | | Next main parameter | and more more more | | + | |
| - | | -> and its sub-parameter | ... descriptions | | + | |
| - | + | ||
| - | |< 100% 30% >| | + | |
| - | ^ Input ^ Description ^ | + | |
| - | | FirstInput | Input Description 1 | | + | |
| - | | SecondInput | Input Description 2 | | + | |
| - | | //ThirdInput// | Input Description 3: Optional Input in Italic | | + | |
| - | + | ||
| - | |< 100% 30% >| | + | |
| - | ^ Output ^ Description ^ | + | |
| - | | FirstOutput | Output Description | | + | |
| - | + | ||
| - | |< 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? | | + | |
| - | + | ||
| - | ==== thisIsTheNameOfMode2 ==== | + | |
| - | 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. | + | |
| |< 100% 30% >| | |< 100% 30% >| | ||
| ^ Parameters ^ Description ^ | ^ Parameters ^ Description ^ | ||
| - | | Some changeable parameter | Description of this parameter | | + | |Amplitude source - //Simulated SAXS data from ribosome// | Use standard curve for sharpening | |
| - | | -> and its sub-parameter | more description | | + | | Amplitude source - //Custom experimental data//| Use reference curve from custom 3d volume for sharpening | |
| - | | Next main parameter | and more more more | | + | | -> Experimental sampling | Pixel size of reference 3d volume in Å| |
| - | | -> and its sub-parameter | ... descriptions | | + | | Filtering mode - //global// | Low-pass filter sharpened 3d volume everywhere to the same resolution level | |
| + | | -> Resolution level | Value for global low-pass filtering in Å| | ||
| + | | Filtering mode - //local// | Low-pass filter sub-regions of the 3d volume map according to local resolution | | ||
| + | | -> Kernel radius | Edge-length of cubic sub-regions in pixels | | ||
| + | | -> Resolution threshold | Lowest resolution to which sub-regions are low-pass filtered | | ||
| + | | Filtering mode - //none// | Omit low-pass filtering of resulting sharpened map | | ||
| + | | Normalize | Check this box to normalize the sharpened 3d volume to mean 0 and sigma 10. | | ||
| + | | Pixel size | Pixel size of the 3d volume to be sharpened. | | ||
| |< 100% 30% >| | |< 100% 30% >| | ||
| ^ Input ^ Description ^ | ^ Input ^ Description ^ | ||
| - | | FirstInput | Input Description 1 | | + | | 3d volume | 3d volume to be sharpened | |
| - | | SecondImput | Input Description 2 | | + | | //Optional experimental data// | Custom 3d volume to be used as reference for sharpening | |
| - | | ThridImput | Input Description 1 | | + | | //Resolution levels// | Local resolution values ("Resolution levels" output) from [[:eyes:logics:FourierShellCorrelation]] logic | |
| + | | //Local resolution map// | Local resolution map ("Fourier shell correlation" output) from [[:eyes:logics:FourierShellCorrelation]] logic | | ||
| |< 100% 30% >| | |< 100% 30% >| | ||
| ^ Output ^ Description ^ | ^ Output ^ Description ^ | ||
| - | | FirstOutput | Output Description | | + | | 1d power spec of input | 1d curve showing the rotationally averaged power spectrum of the input 3d volume | |
| + | | 1d power spec of output | 1d curve showing the rotationally averaged power spectrum of the sharpened 3d volume | | ||
| + | | Sharpened 3D | Sharpened and possibly filtered 3d volume | | ||
| |< 100% 30% >| | |< 100% 30% >| | ||
| ^ New/Changed Header Values ^ Description ^ | ^ New/Changed Header Values ^ Description ^ | ||
| - | | headerValue1 | what does it say? how is it changed? | | + | | pixelSize | Pixel size in Å | |
| - | | 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 ===== | + | ===== Additional Information ===== |
| - | 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 logic is not computationally heavy but needs a lot of RAM for execution. The biggest tested dimensions were 1024x1024x1024 which occupied roughly 12gb of RAM. If not enough RAM is available, this logic will fail to execute. |