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--- pipeline:utilities:start [2018/08/22 12:29]
fmerino
+++ pipeline:utilities:start [2019/04/02 12:45]
lusnig
@@ Line 1: / Line 1: @@
 ===== Utilities =====
+  ; [[pipeline:utilities:sp_batch|Batch Pipeline Execution]] : Run jobs that wait with the execution on each other
   ; [[e2display|Display Data]] : Displays images, volumes, or 1D plots.
   ; [[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.
-  ; [[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
   ; [[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).
-  ; [[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]].
   ; [[sxheader|Header Operations]] : Perform operations on headers of hdf or bdb image file.
   ; [[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.
+  ; [[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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