pipeline:utilities:start

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pipeline:utilities:start [2019/04/02 12:32]
lusnig
pipeline:utilities:start [2019/04/02 12:49] (current)
lusnig
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   ; [[sxpdb2em|PDB File Conversion]] : Converts an PDB atomic model into a simulated density map.  ​   ; [[sxpdb2em|PDB File Conversion]] : Converts an PDB atomic model into a simulated density map.  ​
   ; [[sxrelion2sphire|RELION to SPHIRE Conversion]] : Convert parameters from RELION to SPHIRE formats.   ; [[sxrelion2sphire|RELION to SPHIRE Conversion]] : Convert parameters from RELION to SPHIRE formats.
-  ; [[sxprocess|Adaptive 3D Mask]] : Generates a soft-edged mask for a given volume+  ; [[sp_sphire2relion|SPHIRE to RELION ​ Conversion]] : Convert parameters from SPHIRE to RELION formats
-  ; [[sxprocess|Binary 3D Mask]] : Create a binary 3D mask, e.g. for focused classification+  ; [[pipeline:​utilities:​sp_separate_class|Separate Into Classes]] : Separates stacks of particle images into stacks ​for each class
-  ; [[sxprocess|Change Size of Image or Volume]] ​Resample image or volume to desired pixel size. +  ; [[pipeline:viper:​sp_proj_compare|Compare re-projections]] : Compare re-projections ​to class averages ​ 
-  ; [[e2proc3d|Window Image or Volume]] : Window (pad or clip) image or volume ​to desired dimensions. +  ; [[pipeline:​utilities:​sxpipe_moon_eliminator|Volume Adjustment]] : Resamples, clips, and removes disconnected regions from a 3D map. It optionally creates a mask from the resulting volume. 
-  ; [[sxpipe_moon_eliminator|Moon Eliminator]] : Resamples, clips, and removes disconnected regions from a 3D map. It optionally creates a mask from the resulting volume.+  ; [[pipeline:​viper:​sp_mask|Masking]] : Mask creation tool for 2D or 3D masks 
 +  ; [[sxprocess|Change Size of Image or Volume]] : Change size of image or map 
 +  ; [[https://​blake.bcm.edu/​emanwiki/​EMAN2/​Programs/​e2proc3d|Window Volume]] : Window (pad or clip) volume to the specificy dimension
   ; [[sxpipe_angular_distribution|Angular Distribution]] : Creates a .bild file to display the particle orientation distribution in Chimera.   ; [[sxpipe_angular_distribution|Angular Distribution]] : Creates a .bild file to display the particle orientation distribution in Chimera.
 +  ; [[pipeline:​window:​sp_cryolo_boxmanager|crYOLO - boxmanager]] : Displays boxfiles on images. Allows creation of new training data for crYOLO
 +  ; [[pipeline:​utilities:​sxprocess|Balance Angular Distribution ]] : Balance angular distribution of projection directions by removing excess particles
   ; [[sxprocess|PostRefiner (Single Volumes)]] : Enhancing the power spectrum of any single volumes (Single Volumes Mode).   ; [[sxprocess|PostRefiner (Single Volumes)]] : Enhancing the power spectrum of any single volumes (Single Volumes Mode).
-  ; [[pipeline:​movie:​sxunblur|Micrograph Movie Alignment]] : Align your micrographs using Unblur [[http://​grigoriefflab.janelia.org/​unblur]]. 
   ; [[pipeline:​movie:​sxsummovie|Micrograph Movie Summation]] : Create an average micrograph using Summovie [[http://​grigoriefflab.janelia.org/​unblur]].   ; [[pipeline:​movie:​sxsummovie|Micrograph Movie Summation]] : Create an average micrograph using Summovie [[http://​grigoriefflab.janelia.org/​unblur]].
   ; [[sxheader|Header Operations]] : Perform operations on headers of hdf or bdb image file.   ; [[sxheader|Header Operations]] : Perform operations on headers of hdf or bdb image file.
   ; [[e2bdb|Create Virtual Stack]] : Make a virtual BDB image stack.   ; [[e2bdb|Create Virtual Stack]] : Make a virtual BDB image stack.
   ; [[sxpipe_organize_micrographs|Organize Micrographs/​Movies]] : Move selected micrographs/​movies from source to destination directory.   ; [[sxpipe_organize_micrographs|Organize Micrographs/​Movies]] : Move selected micrographs/​movies from source to destination directory.
 +  ; [[pipeline:​utilities:​sp_ctf_refine|CTF refine (Meridien)]] : Refine the defocus per particle
 +  ; [[pipeline:​utilities:​sp_ctf_refine_stack|CTF refine (Stack)]] : Refine, manual, the defocus per particle
 +
  
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  • Last modified: 2019/04/02 12:32
  • by lusnig