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--- eyes:logics:sharpen3d [2017/06/08 13:36]
jschlie1
+++ eyes:logics:sharpen3d [2017/06/13 15:17] (current)
lschult
@@ Line 2: / Line 2: @@
 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 ("Do not use custom experimental data"; generally more conservative) or using a reference curve from another 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. Therefore, for homogeneously well-resolved maps subsequent filtering can performed in global mode, i.e. every part of the map is low-pass filtered to the same resolution. Heterogeneously resolved maps should be filtered in local mode, i.e. individual regions are filtered according to the respective local resolution.
+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.
-===== Sharpening =====
+===== Process =====
-==== Use custom experimental data ====
-Choose here, whether to sharpen the map based on a standard curve (generally more conservative) or based on a reference volume.
 |< 100% 30% >|
 ^ Parameters                 ^ Description     ^
-| Use  | Use custom reference curve for sharpening  |
+|Amplitude source  - //Simulated SAXS data from ribosome// | Use standard curve for sharpening  |
-| Do not use custom experimental data        | Use standard curve for sharpening |
+| Amplitude source - //Custom experimental data//| Use reference curve from custom 3d volume for sharpening  |
+| -> Experimental sampling        | Pixel size of reference 3d volume in Å|
+| 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.  |
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 ^ Input   ^ Description ^
-| FirstInput  | Input Description 1 |
+| 3d volume  | 3d volume to be sharpened |
-| SecondInput | Input Description 2 |
+| //Optional experimental data//  | Custom 3d volume to be used as reference for sharpening |
-| //ThirdInput//  | Input Description 3: Optional Input in Italic |
+| //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% >|
 ^ 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 |
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 ^ 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? |
-==== 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% >|
-^ 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 |
-| SecondImput | Input Description 2 |
-| ThridImput  | Input Description 1 |
-|< 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? |
-=====Parameters=====
-===Experimental Sampling [Å]===
-The pixel size of the input “Optional experimental data” [in Angstrom]. If no experimental data input is given, this value is not used.
-===Fill filter with zeros===
-Check this checkbox to fill the filter image with zeros at indexes that are outside the important diameter. Otherwise the filter image will be filled using constant extrapolation.
-===Normalize===
-Check this checkbox to normalize the corrected 3d volume to mean 0 and sigma 10.
-===Pixel size [Å]===
-The pixel size of the input “3d volume” [in Angstrom].
-===Resolution Cutoff [px]===
-Cut off resolution in pixel (from 0 to volume radius). 0 = no cutoff
-===Resolution level [Å]===
-The target resolution level [in Angstrom]
-=====Inputs=====
-===Optional experimental data===
-Provides a reference 3d structure which is used instead of the spider x-ray curve for correction
-===3d volume===
-Provides the 3d volume to be sharpened
-=====Outputs=====
-===1d rot avg of power spec===
-d curve showing the 1d averaged power spectrum of the input 3d volume
-===Enhancement curve===
-d curve showing the 1d representation of the output “Amplitude filter”.
-===Amplitude filter===
-d volume that shows the applied sharpening filter image.
-===Amplitude Corrected 3d volume===
-Contains the corrected output 3d volume.
-==Written Header Values==
-  * **resolutionLevel** Resolution where cut off was performed
-  * **pixelSize** Pixel size of the volume
 ===== Additional Information =====
 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.