Xmipp
v3.23.11-Nereus
Modules
Here is a list of all modules:
[detail level
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Libraries
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Basic data library
X-Ray Microscope PSF class
AFT Library
Alignment Estimation
Alignment Result
Array2D
Basic PCA class
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Basis function
Blobs
Splines
BSplineGrid
CPU support class
CTF support classes
Dimensions
FFTSettings
Filters
Projections (2D Image + Euler angles)
Grids
HW
Mathematical operations of images and volumes
Image Resize class
Numerical integration
Local Alignment Result
Masks
Micrographs
Resolution
Mathematical morphology
Normalization of images and volumes
Numerical Tools
Phantoms
Point
Point2D
Point3D
Polar coordinates
Parameters Projection for Tomography
Rectangle
Rotational spectrum
sampling (Sampling the projection sphere)
Spherical Harmonics
Steerable filters
Symmetries
Transform Geometry
UnitCell
Vector volumes
Wavelets
Image Convert
Polynomials
Document Files (Docfiles)
Python Utils
Selection files (Selfiles)
Some extensions related with Xmipp programs
Arguments parsing
Arguments parser
Geometry
Histograms
Matrix1D Vectors
Matrix2D Matrices
Metadata Stuff
Extension to Metadata Stuff
Multidimensional Arrays
Symmetry handling
Geometrical transformations
Datatypes for MultidimArrays
Error handling
Fourier transforms
FFTW Fourier transforms
General functions
for General Purpose handling of hdf5 files
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Images
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Image Formats
DM3 File format
DM4 File format
HDF5 File format
Imagic File format
INF File format
MRC File format
RAW Data type
RAW File format
Stochastic Proximity Embedding
Spider File format
TIA File format
TIFF File format
Extension to Image class
Macros
Memory management for numerical recipes
Basic structure for Xmipp programs
String utilities
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Reconstruction library
Homogenizer
art_xray (ART for xrays)
Classify Kmeans 2D
Classify a set of images into a discrete set of classes
Common Lines (find common lines between projections)
ctf_correct_idr (Iterative Data Refinement for CTF amplitude correction)
(phase flipping)
Evaluate Coordinates
Extracting Particles From Metadata
IDR Xray Tomography
Make spectra
ml_refine3d (Maximum likelihood 3D refinement)
Maximum likelihood for tomograms
Construct a low and high resolution dictionary
Restore a volume with a low/high dictionary
project_xr (project for tilt series)
Reconstruct Alternating Direction Method of Multipliers
reconstruct_art_pseudo (Reconstruct with pseudo atoms)
Program ART
Measure resolution through the inverse of border widths
resolution_ssnr (Spectral Signal to Noise Ratio)
score_micrograph (Evaluates the score of a micrograph)
Align two dual tilt series
angular_assign_for_tomogram (Discrete angular assignment for tomography)
angular_assign_for_tilt_series
Tomo Extract Subvolume
Remove fluctuations in tilt series
align_tilt_pairs (Align tilted and untilted images in a random conical tilt experiment)
Enhance constrast
Volume PCA
Validation of volume consistency with respect to the provided classes
Xray import
GPU Correlation
GPU MultidimArray At CPU
Fourier reconstruction
Resolution
FFTwT
Masks in Fourier space
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Fourier projection
Projections (2D Image + Euler angles)
Micrograph Downsample
Core analysis for CL2D
Classification with Fourier Transform based Translational and Rotational Invariants
Rotational invariant PCA
Alignment Estimation
adjust_volume_grey_values (Adjust volume grey values to a set of projections)
ExtremaFinder
GeoTransformerSettings
align2d (Align a set of 2D images)
MeritSettings
accuracy to angular assignment by pca
AngularAssignmentMag
angular_distance (Distance between two angular assignments)
angular_common_lines
angular_continuous_assign (Continuous angular assignment)
angular_continuous_assign2 (Continuous angular assignment)
angular_discrete_assign (Discrete angular assignment)
Estimate the tilt axis position in a pair of micrographs
angular_neighbourhood (Projection neighbourhood)
new_projmatch (Discrete angular assignment using a new projection matching)
Rotation Estimation Setting
art_crystal (ART for crystals)
AShiftCorrEstimator
AShiftEstimator
ART Reconstruction stuff
Parameters and common ART Reconstruction stuff
BSpline Transform Settings
BSplineHelper
Compare Classes
Evaluate Classes
ProgExtractFeatures
Classification first split
Deform a volume using spherical harmonics
Coordinates Micrograph Filter
Correlation Computer
CTF Phase flip in 2D particles
ctf_correct_amplitude3D (3D Wiener filtering)
psd_enhance (Enhance visualization of the PSD)
ctf_estimate_from_micrograph (CTF estimation from a micrograph)
adjust_ctf (Adjust CTF parameters to PSD)
Program CTF Basic Parameters
adjust_ctf (Adjust CTF parameters to PSD)
Spectrum modelling by ARMA filters
ctf_group
psd_Sort (Sort visualization of the PSD)
Image denoising
Operations for projection directions
Alignment with Normal modes
Routines to work with fringes
Image Assignment Tilt Pair
Eliminate images whose energy is extremely large or extremely low
Eliminate Empty Particles
Even
Image sort by statistics
Iterative Alignment Estimator
Split a metadata according to a 3D volume
Image denoising
ml_align2d (Maximum likelihood in 2D)
mlf_align2d (Maximum likelihood in 2D in Fourier space)
Movie alignment correlation
Movie Alignment Correlation
Estimate gain from a movie
Movie alignment by correlation
Multireference Aligneability
Alignment of volumes with Normal modes
Different statistics of the PDB
convert_pdb2vol (PDB Phantom program)
Deform PDB according to NMA
Pdb Reduce
Phantom Movie
phantom_simulate_microscope (Microscope simulation)
Polar Rotation Estimator
precompute_sampling (Precompute samplin points in the projection sphere)
Filter Operation
Image Residuals
Estimate the SSNR
project (Generate projections from a volume)
project_crystal (Project crystals)
projectTomograpy (project for tilt series)
PSD Estimator
radon (Radon transform)
Reconstruct multiple volumes analyzing significant correlations
reconstruct_wbp (Weighted Back Projection)
refinement (Shift refinement)
Local Filter
Shift Correlation Estimator
Single Extrema Finder
Subtomogram subtraction
Subtract projections
symmetrize (Symmetrize a volume or image)
Threshold
Change the image gray values to match a volume projection
without tilt
Restoration of a volume given two halves
Heuristic Initial Volume
Sharpening
Volume segmentation
ConvertVol2Pseudo
Volume Set Align
Align Significant GPU
Volume Halves Restoration GPU
Cuda BSpline GeoTransformer
Cuda Correlation Computer
CudaFFT
Cuda GPU Correlation
GeoShift Transformer
Cuda GPU GeoTransformer
Cuda GPU Reconstruct Fourier
Cuda Rotation Polar Estimator
CudaShiftCorrEstimator
CudaExtremaFinder
Volume Halves Restorator
Volume Restoration Kernels
Cuda Xmipp Utils
GPU
Detect missing wedge
Tomo map back
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Classification library
Agglomerative Hierarchical Clustering
Analyze cluster
Base Algorithm
Batch training of Kohonen SOM algorithm
Code book
Data sets
Some type definitions
Fuzzy c-means clustering algorithm
Fuzzy Kohonen Clustering Network algorithm
Fuzzy code book
Smoothly Distributed Fuzzy c-means Self-Organizing Map algorithm
Smoothly Distributed Gaussian Kernel Probability Density Estimator Self Organizing Map
Kendersom: Smoothly Distributed Kernel Probability Density Estimator Self Organizing Map
Classifier
kSVD
Self Organizing Map
Fuzzy Self Organizing Map
SOM Layouts
Naive Bayes Classifier
Principal Component Analysis
Sammon Projection
Kohonen Self Organizing Maps
SVM Classifier
Training Sets
Training Vectors (Feature vectors) class
Vector Operations
Vector Quantization for Projections
Vector Quantization for Volumes
Graphics library
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Interface library
PDB
Spider
Virus
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Bilib library
Spline transform
Fourier Transform
Hartley Transform
Find root
FIR Convolve
Fourier Convolve
Bilib Geometry
Poles of B-spline and Omom
Gradient
Histograms
IIR Convolve
Spline interpolation
Kernel definition
Kernel derivatives
Kernel integrals
Linear algebra
Morphology
Moving average
Polynomial
Pyramid filters
Pyramid tools
Swap axes in a volume
Signal processing windows
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Parallel library
(MPI)
Reconstruct using ADMM (MPI)
Determine the angular determination accuracy of a set of particles and a 3D reconstruction (MPI)
(MPI)
MPI Angular Class Average
validate a volume analyzing the clusterability of each projection image (MPI)
NMA Alignment for volumes with MPI parallelization
MPI Performance Test
Reconstruct multiple volumes analyzing significant correlations (MPI)
MPI
Threads
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Dimensionality reduction library
Diffusion Maps
Tools for dimensionality reduction
Gaussian Process Latent Variable Model
Hessian Local Linear Embedding
Kernel PCA
Laplacian Eigenmap
Linear Local Tangent Space Alignment
Linearity Preserving Projection
Local Tangent Space Alignment
Project a matrix onto a lower dimensionality space
Component Analysis
Principal Component Analysis
Probabilistic PCA
Stochastic Proximity Embedding
Obtain image distances between images in metadata
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Programs
ProgMPIXrayProject
MpiProgAngularProjectionMatching
MPI_ML
ProgMPIReconsArt
ProgMPIRecFourier
ProgMPIRecWbp
MPI Volume Set Align
Movie Alignment Correlation GPU
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