List of all Xmipp programs

Note that from Xmipp-2.0 onwards, the names of many Xmipp programs have changed. Click here to see a table relating the new names with the old ones. For now, both the old and the new names will keep on working (a warning will appear when using an old name). In the next release, the old names will disappear.

By Topic

Micrographs

• testing_wiki Testing wiki generation
• convert_tiff2raw Converts scanner tiff files to raw format (Obsolete, will be removed in Xmipp 3 .0)
• micrograph_denoise Denoising of the raw micrographs
• micrograph_downsample Downsampling of the raw micrographs
• micrograph_mark Manual particle picking for single micrographs and tilt pairs
• micrograph_particle_picker Particle picker to generate image stacks used on 3D reconstruction.
• micrograph_scissor Window-out manually selected particles in single-file Spider format
• micrograph_window Apply a window to raw micrographs
• micrograph_phase_flipping Correct CTF phases (using phase flipping) (similar to ctf_correct_phase but handles microgrphs)

CTF estimation and correction

• ctf_estimate_from_micrograph Estimate CTF parameters for a micrograph
• ctf_create_ctfdat Create a CTFdat file from image selfiles for each micrograph
• ctf_correct_idr Correct CTF amplitudes (using Iterative Data Refinement)
• ctf_correct_phase Correct CTF phases (using phase flipping)
• ctf_correct_amplitude2d Correct CTF amplitudes (using Van Cittert's iterations)
• ctf_group Automatically create CTF groups from a single CTFdat file
• ctf_profile Plot the profile of a CTF
• ctf_view Visualize CTF fitting
• psd_enhance Enhance power spectral density Thon rings

Selection files, Document files

• metadata_operate Arithmetic operation using metadata columns.
• docfile_append Concatenate two docfiles
• docfile_histogram Computes the histogram of a docfile column
• docfile_select_subset Make a docfile of a subset given in a selfile
• selfile_compare Compare two selfiles (overlap, differences etc)
• selfile_copy Copy images in a selfile to a different location
• selfile_create Create a selfile
• selfile_delete Remove the images in a selfile
• selfile_move Move images in a selfile to a different location
• selfile_select Select images from a selfile based on a condition in a docfile
• selfile_split Split selfile in random subsets
• selfile_statistics Produces statistics about the images in a selfile
• selfile_subset Produce random subsets of any size
• filter_projections Select projections from a selfile meeting a number of quality criteria

Image header manipulation

Please read the important Note on image headers.

• header_assign Sets angles, translations and weights to the headers of 2D-images
• header_extract Gets angles, translations and weights from the headers of 2D-images
• header_reset Resets the headers of 2D-images, it can be used also for setting tilt series tilt angles
• header_print Prints header information to the screen

Images

• align2d 2D-alignment of images
• center_image Center images
• align_tilt_pairs Align tilted images for random conical tilt reconstruction
• average Returns the average and standard deviation of a set of images or volumes
• correlation Calculate correlation coefficient, euclidean distance & mutual information between images
• denoise Denoise an image or volume
• find_center2d Find center of mass and symmetry elements of an image
• fourier_filter Filter an image or volume
• fourier_transform Compute the amplitude or phase of the Fourier Transform of an image or volume
• header_apply Apply header stored geometric transformation
• histogram Computes the histogram of an image or volume
• make_spectra Compute rotational spectra
• mask Apply a mask, create a mask, create a blank image and voxel counting
• mean_shift Filter image by means of the mean-shift algorithm
• mask_design Design a mask graphically
• mirror Flip (mirror) an image or volume
• morphology Apply morphological filters to an image or a volume
• normalize Normalizes pixel values for images/volumes
• operate Apply algebraic operations to images or volumes
• range_adjust Adjust the grey range
• resolution_fsc Estimate high-resolution limit of a set of images using FRC or DPR
• series_remove_fluctuations Remove flickering in a tilt series
• resolution_ssnr Estimate the 3D and volumetric Spectral Signal-to-Noise Ratio
• reverse_endian Reverses the endian status of the image or volume
• rotate Rotate an image or a volume
• scale Scales an image or volume to a new size by interpolation
• scale_pyramid Image pyramids
• shift Shift an image or a volume
• show Visualize images, volumes, sel files, spectras, soms...
• sort_by_statistics Sort images based on simple statistics (to identify junk particles)
• statistics Prints image/volume statistics (avg, stddev, min & max) to the screen
• threshold Threshold operations (density value conditions, distance conditions and binarization possibility)
• window Cuts or expands images

Volumes

• align_volumes Align two volumes
• adjust_volume_grey_levels Linear transformation of the gray values of a volume
• convert_voxels22blobs Conversion from a voxel volume to a blob volume and viceversa
• correct_bfactor Sharpen maps through B-factor correction
• create_projection_library Create gallery of projections, specially thought for projection matching
• detect_missing_wedge Detect the orientation of the missing wedge in a tomogram
• find_center3d Find center of mass and symmetry elements of a volume
• mean_shift Filter volume by means of the mean-shift algorithm
• project Project a phantom/volume/PDB
• projection_real_shears Project a Xmipp or Spider volume
• project_tomography Project a volume for tomography
• reconstruct_art and mpi_reconstruct_art 3D algebraic (iterative) reconstruction from projections
• reconstruct_wbp and mpi_reconstruct_wbp 3D-Reconstruction using weighted back-projection (arbitrary geometry)
• reconstruct_fourier and mpi_reconstruct_fourier 3D-Reconstruction using direct Fourier methods (arbitrary geometry)
• resolution_fsc Estimate high-resolution limit using FRC or DPR between 2 volumes
• separate_objects Separate connected objects from a binary volume
• symmetrize Symmetrize a volume
• volume_segment Segment a volume to a given mass
• xray_project Project a volume for X-rays tomography

Classification

• classify_analyze clusters Analyze the compactness of a cluster
• classify_batch_som Kohonen Self-Organizing Map using Batch training
• classify_CL2D Divide a set of images into a given number of classes
• classify_CL2D_sort_images Sort a number of classes computed with classify_CL2D
• classify_fcmeans Fuzzy C Means
• classify_fkcn Fuzzy Kohonen Clustering Networks
• classify_fsom Fuzzy Self Organizing Maps
• classify_kcmeans Kernel Probability Density Estimator Clustering algorithm
• classify_kerdensom Kernel Density Self Organizing Map
• classify_pca Principal Components Analysis
• classify_project_pca Project data using PCA
• classify_sammon_projection Sammon projection algorithm
• classify_som Kohonen Self Organizing Maps
• convert_data2descr Converts a data file into a phantom description file
• convert_data2img Convert data format to images
• convert_data2pdb Converts a data file into a PDB file
• convert_data2vol Convert data format to volumes
• convert_img2data Convert images to data format
• convert_vol2data VConvert data format to volumes
• convert_vol2pseudo Gets a list of voxel coordinates from a Xmipp volume
• ml_align2d and mpi_ml_align2d 2D-classification and alignment by maximum-likelihood (ML2D)
• ml_refine3d and mpi_ml_refine3d 3D-classification and angular assignment by maximum-likelihood (ML3D)
• mlf_align2d and mpi_mlf_align2d 2D-classification by maximum-likelihood in Fourier space (MLF2D)
• mlf_refine3d and mpi_mlf_refine3d 3D-classification by maximum-likelihood in Fourier space (MLF3D)
• ml_tomo 3D-classification and alignment of subtomograms or RCT reconstructions by maximum-likelihood
• tomo_extract_subvolume Extract subvolumes out of (ml_tomo-) aligned subtomograms (e.g. virus vertices)

Angular assignment

• angular_commonline Provide an initial angular assignment for class averages without any reference volume
• angular_continuous_assign Continous assignment of Euler angles (by spline interpolation)
• angular_discrete_assign Assigns Euler angles to projection images
• angular_distribution_show Makes a picture of the Ewald-sphere and the angular distribution of a projection set
• angular_distance Computes the distance between two angle sets
• angular_neighbourhood Group images in defined projection direction neighbourhoods
• angular_projection_matching and mpi_angularprojection_matching Projection matching using fast 3D+2D rotational+translational search

Phantoms

• add_noise Add noise to an image or volume
• convert_pdb2descr Creates a phantom description file from a PDB file
• convert_pdb2vol Convert a PDB file to a volume
• phantom_create Create volumes from mathematical description
• phantom_simulate_microscope Simulate the effect of the microscope for projections
• phantom_create_micrograph Creates a phantom micrograph
• phantom_transform Translate, rotate, or scale a Xmipp phantom or a PDB
• pdbphantom Generate a Xmipp volume from a PDB or MMOL file
• project Project a phantom/volume/PDB
• project_tomography Project a volume for tomography
• surface Simulates an AFM-like surface
• xray_project Project a volume for X-rays tomography
• transform_add_noise Add noise to an image or volume

Crystals

• crystal_angular_projection_matching Assign angles to crystal projections using a reference projection library
• crystal_aph2img Creates images from 2D crystal spots
• crystal_create_surface Creation of a lattice in a parabolic surface
• crystal_lattice_vectors Manages lattice vector conversion between MRC and Xmipp
• crystal_shear Deform a volume by a linear transformation defined by a 2x2 matrix
• crystal_unbend Crystal Unbending

Interaction with other programs

• adapt_for_spider Several operations to create spider files
• convert_dm32raw Convert dm3 (digital micrograph) images to raw format (Obsolete, will be removed in Xmipp 3 .0)
• convert_img2jpg Convert a Spider image into Jpeg
• convert_image Convert between many image formats (Xmipp 3.0)
• convert_raw22spi Convert raw images to/from spider format. Together with Imagemagick, any image format can be addressed (Obsolete, will be removed in Xmipp 3 .0)
• convert_spi22ccp4 Convert from/to CCP4/MRC MAP volumes/images (Obsolete, will be removed in Xmipp 3 .0)
• convert_spi22em Convert from/to EM-format volumes (used in the TOM toolbox)
• convert_stack22images Convert from/to spider stacks of images to volumes or set of images
• convert_tia2raw Convert tia (Tecnai Imaging and Analysis) images to raw format (Obsolete, will be removed in Xmipp 3 .0)
• convert_vol2jpg Convert a Spider volume into Jpeg

Tomography

• angular_align_dual_tilt_series Marker free alignment of two dual single-axis tilt series
• angular_assign_for_tilt_series Marker free projection alignment for single axis tilt series
• xray_import Import a tilt series taken by the X-ray microscope
• project_xr Project a volume for X-rays tomography
• xray_psf_create Precompute the PSF for X-ray tomography