▼Libraries  
►Basic data library  
AFT Library  
Alignment Estimation  
Alignment Result  
Array2D  
Basic PCA class  
►Basis function  
Blobs  
Splines  
BSplineGrid  
CPU support class  
CTF support classes  
Dimensions  
FFTSettings  
FFTSettingsNew  
Filters  
Projections (2D Image + Euler angles)  
Grids  
HW  
Mathematical operations of images and volumes  
Image Resize class  
Numerical integration  
Local Alignment Result  
Masks  
Micrographs  
Monogenic Signal  
Mathematical morphology  
Normalization of images and volumes  
Numerical Tools  
Phantoms  
Point  
Point2D  
Point3D  
Polar coordinates  
Parameters Projection for Tomography  
XRay Microscope PSF class  
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  
►Images  
►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  
►Reconstruction library  
Homogenizer  
Masks in Fourier space  
►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)  
align_tilt_pairs (Align tilted and untilted images in a random conical tilt experiment)  
MeritSettings  
accuracy to angular assignment by pca  
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)  
art_xray (ART for xrays) 

AShiftCorrEstimator  
AShiftEstimator  
ART Reconstruction stuff  
Parameters and common ART Reconstruction stuff  
BSpline Transform Settings  
BSplineHelper  
Compare Classes  
Evaluate Classes  
ProgExtractFeatures  
Classification first split  
Classify Kmeans 2D  
Classify a set of images into a discrete set of classes  
Common Lines (find common lines between projections)  
Coordinates Micrograph Filter  
Correlation Computer  
ctf_correct_idr (Iterative Data Refinement for CTF amplitude correction)  
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  
(phase flipping)  
psd_Sort (Sort visualization of the PSD)  
Image denoising  
Operations for projection directions  
Evaluate Coordinates  
Extracting Particles From Metadata  
FFTwT  
Alignment with Normal modes  
Routines to work with fringes  
IDR Xray Tomography  
Image Assignment Tilt Pair  
Eliminate images whose energy is extremely large or extremely low  
Eliminate Empty Particles  
Even  
Make spectra  
Image sort by statistics  
Iterative Alignment Estimator  
Split a metadata according to a 3D volume  
Image denoising  
ml_align2d (Maximum likelihood in 2D)  
ml_refine3d (Maximum likelihood 3D refinement)  
Maximum likelihood for tomograms  
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  
Construct a low and high resolution dictionary  
convert_pdb2vol (PDB Phantom program)  
Deform PDB according to NMA  
Pdb Reduce  
Restore a volume with a low/high dictionary  
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)  
project_xr (project for tilt series)  
PSD Estimator  
radon (Radon transform)  
Reconstruct Alternating Direction Method of Multipliers  
Program ART  
reconstruct_art_pseudo (Reconstruct with pseudo atoms)  
Fourier reconstruction  
Reconstruct multiple volumes analyzing significant correlations  
reconstruct_wbp (Weighted Back Projection)  
refinement (Shift refinement)  
Monogenic Signal  
Measure resolution through the inverse of border widths  
Local Filter  
resolution_ssnr (Spectral Signal to Noise Ratio)  
score_micrograph (Evaluates the score of a micrograph)  
Shift Correlation Estimator  
Single Extrema Finder  
symmetrize (Symmetrize a volume or image)  
Threshold  
Align two dual tilt series  
angular_assign_for_tomogram (Discrete angular assignment for tomography)  
angular_assign_for_tilt_series  
Detect missing wedge  
Tomo Extract Subvolume  
Tomo map back  
Remove fluctuations in tilt series  
Change the image gray values to match a volume projection  
without tilt  
Deform a volume using spherical harmonics  
Enhance constrast  
Restoration of a volume given two halves  
Heuristic Initial Volume  
Sharpening  
Volume PCA  
Volume segmentation  
ConvertVol2Pseudo  
Validation of volume consistency with respect to the provided classes  
Volume Set Align  
Xray import  
Align Significant GPU  
Volume Halves Restoration GPU  
GPU Correlation  
GPU MultidimArray At CPU  
Cuda BSpline GeoTransformer  
Cuda Correlation Computer  
CudaFFT  
Cuda GPU Correlation  
GeoShift Transformer  
Cuda GPU GeoTransformer  
Cuda GPU movie Alignment Correlation  
Cuda GPU Reconstruct Fourier  
Cuda Rotation Polar Estimator  
CudaShiftCorrEstimator  
CudaExtremaFinder  
Volume Halves Restorator  
Volume Restoration Kernels  
Cuda Xmipp Utils  
GPU  
►Classification library  
Agglomerative Hierarchical Clustering  
Analyze cluster  
Base Algorithm  
Batch training of Kohonen SOM algorithm  
Code book  
Data sets  
Some type definitions  
Fuzzy cmeans clustering algorithm  
Fuzzy Kohonen Clustering Network algorithm  
Fuzzy code book  
Smoothly Distributed Fuzzy cmeans SelfOrganizing 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  
►Interface library  
PDB  
Spider  
Virus  
►Bilib library  
Spline transform  
Fourier Transform  
Hartley Transform  
Find root  
FIR Convolve  
Fourier Convolve  
Bilib Geometry  
Poles of Bspline 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  
►Parallel library  
(MPI)  
Determine the angular determination accuracy of a set of particles and a 3D reconstruction (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 using ADMM (MPI)  
Reconstruct multiple volumes analyzing significant correlations (MPI)  
MPI  
Threads  
►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  
▼Programs  
MpiProgAngularProjectionMatching  
MPI_ML  
ProgMPIXrayProject  
ProgMPIReconsArt  
ProgMPIRecFourier  
ProgMPIRecWbp  
MPI Volume Set Align  
Movie Alignment Correlation GPU  