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> relion_image_handler --help
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input STAR file, image (.mrc) or movie/stack (.mrcs)
--o () : Output name (for STAR-input: insert this string before each image's extension)
====== image-by-constant operations =====
--multiply_constant (1) : Multiply the image(s) pixel values by this constant
--divide_constant (1) : Divide the image(s) pixel values by this constant
--add_constant (0.) : Add this constant to the image(s) pixel values
--subtract_constant (0.) : Subtract this constant from the image(s) pixel values
--threshold_above (999.) : Set all values higher than this value to this value
--threshold_below (-999.) : Set all values lower than this value to this value
====== image-by-image operations =====
--multiply () : Multiply input image(s) by the pixel values in this image
--divide () : Divide input image(s) by the pixel values in this image
--add () : Add the pixel values in this image to the input image(s)
--subtract () : Subtract the pixel values in this image to the input image(s)
--fsc () : Calculate FSC curve of the input image with this image
--power (false) : Calculate power spectrum (|F|^2) of the input image
--adjust_power () : Adjust the power spectrum of the input image to be the same as this image
--fourier_filter () : Multiply the Fourier transform of the input image(s) with this one image
====== additional subtract options =====
--optimise_scale_subtract (false) : Optimise scale between maps before subtraction?
--optimise_bfactor_subtract (0.) : Search range for relative B-factor for subtraction (in A^2)
--mask_optimise_subtract () : Use only voxels in this mask to optimise scale for subtraction
====== per-image operations =====
--stats (false) : Calculate per-image statistics?
--com (false) : Calculate center of mass?
--bfactor (0.) : Apply a B-factor (in A^2)
--lowpass (-1.) : Low-pass filter frequency (in A)
--highpass (-1.) : High-pass filter frequency (in A)
--directional () : Directionality of low-pass filter frequency ('X', 'Y' or 'Z', default non-directional)
--LoG (-1.) : Diameter for optimal response of Laplacian of Gaussian filter (in A)
--angpix (-1) : Pixel size (in A)
--rescale_angpix (-1.) : Scale input image(s) to this new pixel size (in A)
--force_header_angpix (-1.) : Change the pixel size in the header (in A). Without --rescale_angpix, the image is not scaled.
--new_box (-1) : Resize the image(s) to this new box size (in pixel)
--filter_edge_width (2) : Width of the raised cosine on the low/high-pass filter edge (in resolution shells)
--flipX (false) : Flip (mirror) a 2D image or 3D map in the X-direction?
--flipY (false) : Flip (mirror) a 2D image or 3D map in the Y-direction?
--flipZ (false) : Flip (mirror) a 3D map in the Z-direction?
--invert_hand (false) : Invert hand by flipping X? Similar to flipX, but preserves the symmetry origin. Edge pixels are wrapped around.
--shift_com (false) : Shift image(s) to their center-of-mass (only on positive pixel values)
--shift_x (0.) : Shift images this many pixels in the X-direction
--shift_y (0.) : Shift images this many pixels in the Y-direction
--shift_z (0.) : Shift images this many pixels in the Z-direction
--avg_ampl (false) : Calculate average amplitude spectrum for all images?
--avg_ampl2 (false) : Calculate average amplitude spectrum for all images?
--avg_ampl2_ali (false) : Calculate average amplitude spectrum for all aligned images?
--average (false) : Calculate average of all images (without alignment)
--correct_avg_ampl () : Correct all images with this average amplitude spectrum
--minr_ampl_corr (0) : Minimum radius (in Fourier pixels) to apply average amplitudes
--remove_nan (false) : Replace non-numerical values (NaN, inf, etc) in the image(s)
--replace_nan (0) : Replace non-numerical values (NaN, inf, etc) with this value
--phase_randomise (-1) : Randomise phases beyond this resolution (in Angstroms)
====== 3D operations =====
--sym () : Symmetrise 3D map with this point group (e.g. D6)
====== 2D-micrograph (or movie) operations =====
--flipXY (false) : Flip the image(s) in the XY direction?
--flipmXY (false) : Flip the image(s) in the -XY direction?
--add_edge (false) : Add a barcode-like edge to the micrograph/movie frames?
--edge_x0 (0) : Pixel column to be used for the left edge
--edge_y0 (0) : Pixel row to be used for the top edge
--edge_xF (4095) : Pixel column to be used for the right edge
--edge_yF (4095) : Pixel row to be used for the bottom edge
====== Movie-frame averaging options =====
--avg_bin (-1) : Width (in frames) for binning average, i.e. of every so-many frames
--avg_first (-1) : First frame to include in averaging
--avg_last (-1) : Last frame to include in averaging
--average_all_movie_frames (false) : Average all movie frames of all movies in the input STAR file.
====== PNG options =====
--black (0) : Pixel value for black (default is auto-contrast)
--white (0) : Pixel value for white (default is auto-contrast)
--sigma_contrast (0) : Set white and black pixel values this many times the image stddev from the mean
--colour_fire (false) : Show images in black-grey-white-red colour scheme (highlight high signal)?
--colour_ice (false) : Show images in blue-black-grey-white colour scheme (highlight low signal)?
--colour_fire-n-ice (false) : Show images in blue-grey-red colour scheme (highlight high&low signal)?
--colour_rainbow (false) : Show images in cyan-blue-black-red-yellow colour scheme?
--colour_difference (false) : Show images in cyan-blue-black-red-yellow colour scheme (for difference images)?
--version : Print RELION version and exit