Releases xmipp program

3.24.12 - Poseidon

Xmipp Programs

  • New programs

    • tomo_average_subtomos: This method carries out a subtomogram averaging. It means, given a set of subtomogram the program will estimate the average map

    • denoising_tv: The program will make denoising using total variation

    • tomo_ctf_wiener2d_correction: This method performs a CTF correction of a tilt series

    • angular_continuous_assign2_gpu: Make a continuous angular assignment with GPU

    • cuda_fourier_projection

    • predict_deep_center

    • cl2d_clustering

  • Programs updated

    • tomogram_reconstruction: averaging with gold standard, tigre with internal interpolation, enviroment of tigre updated

    • mpi_subtract_projection / subtract_projection: Improvements on projection subtraction a particle boosting both in MPI and single thread version

  • Programs fixed

    • resolution_directional

    • ctf_estimate_from_psd: Bug fix with no defocus

    • mpi_subtract_projection / subtract_projection: subtraction a particle boosting both in MPI and single thread version

    • volume_halves_restoration_gpu: Fixed failure when using masks

Installation and user guide

  • Total new installer based on CMake. More robust and simplified

  • New posting of statistics about installations

  • Allow re-compilation without internet

  • Added next generation of libstdcxx to DLTKv0.3 env to enhance compatibility

  • Forcing to compile Xmipp with the libstdc++ availabe in the scipion3 env if exist

More Xmipp

  • Added support for reading EER

  • Handling .gain files correctly

  • Added MADV_HUGEPAGE support check

  • Fix for rare axis orderings in MRC/MAP files

  • Local average label added (used to measure the intensity of the particles in the original micrographs)

3.24.06 - Oceanus

Xmipp Programs

  • New programs

    • xtomo tigre reconstruction: This program provides a variety of algorithms to reconstruct tomogram from a set of tilt series

    • graph_max_cut: split volume program

    • tomo_simulate_tilt_series: simualtion of ts, tomograms and coordinates

  • Programs updated

    • Deep_center: interface simplified, calculate shift for particles

    • deep_misalignment_detection: update model

    • pdb_label_from_volume:Added CIF format support

    • resolution_monotomo: Fast subtomo extraction

    • resolution_monotomo: accelarating monotomo with float

    • tomogram_reconstruction: tigre reconstruction added

    • tomo_extract_subtomograms: solving some bugs and enhancing performance

    • tomo_extract_particlestacks: solving some bugs and enhancing performance

  • Programs fixed

    • movie_estimate_gain: Initialize sigma values

    • resolution_localfilter: double not integer

    • movie_estimate_gain: Initialize sigma values

    • project_tomography: internal loop

    • pdb: Fixed PDB write function when no categories are present

    • fourier_filter:Fix WEDGE option in FourierFilter

    • resolution_pdb_bfactor:fix unaccounted column in res bfac pdb

    • fourier_filter: Fixing missing cone

Installation and user guide

  • Fixed PyXmipp installation

  • Update pythorch version on DLTK pyTorch enviroment

  • Fix DLTK installation

  • Removed force flag on conda installations (new conda version)

More Xmipp

  • API for collecting xmipp installation statistics

  • Local average added: Now the micrograph scissor annotates the local intensity value around the particles in the original micrographs.

  • Added support for half precision float micrographs

  • Wipe out memory ouptut in cuFFT

  • Deprecated deep_denoising

  • Fix for rare axis orderings in MRC/MAP files

  • Adding fixed extension to tomo

3.23.11 - Nereus

Xmipp Programs

  • New programs

    • local_volume_adjustment: This program modifies a volume in order to adjust its intensity locally to a reference volume

    • subtomo_subtraction: New program with mpi version

  • Programs updated

    • tomo_extract_subtomogram: Accept target box size

    • convert_from_pdb: Added cif support

    • phantom_movies: Adding more options: circle and cross

    • angular_neighbourhood: Modified to output the result in the best symmetry group

    • batch_deep_misalignment: Detection: GPU option

  • Programs fixed

    • volume_from_pdb: Bug fix in dealing with orig=0, Detection of contrast inverted maps

    • tomo_extract_particles: Stack fixes, dose fixes

    • image_convert: Fixed issue when providing a metadata file as input

    • volume_substraction: Change NaNs generated by a division between 0 by 0s.

Installation and user guide

  • Disabled downloading 380MB file not required

  • Clarifying the requirements

  • More robust thread execution in the installator

  • Fixed bug collecting versions

  • Removed auto updater from libcifpp

More Xmipp

  • Upgraded CUDA toolkit in DLTK 1.0

  • Fix PDB read: This fixes a bug where pdbs whose atom name start in position 12 (in base 0)

  • CUDA 12.2 supported (not full tested)

  • Fixed PDB reading for shorter PDBs

  • Allow not compiling xmipp to debug changes in python scripts

  • Xmipp will now be able to read any volume with any values of those fields correctly.

  • Fixed pixel size not being properly stored

  • Fixed MetaData to avoid dangling references

  • Added compatibility for undefined axis sequences in MRC files

  • Added option to write mirrors in angularDistance

3.23.07 - Morpheus

Xmipp Programs

  • New programs: image_peak_high_contrast(for detecting high contrast regions in tomographic reconstruction)

  • misaligment_detection (to detect misalignment in tomographic reconstructions from high-contrast regions)

  • deep_global_assignment

  • deep_center

  • Programs updated

  • xmipp_angular_distance: new features - tomo_extract_particles: new features

  • subtract_projection: parallelization with mpi

  • tomo_extract_subtomograms: allow downsampling of features

  • angular_resolution_alignment: Detect misalignment with resolution

  • Programs fixed

  • align_volume_and_particles: Fixed error

  • angular_project_library: Removed deterministic behaviour (mpi)

  • volumen_subtraction: fixed bug - Deprecated programs (For more details visit)

  • classify_kmeans_2D - rotational_spectra - particle_boxsize

Installation and user guide

  • New clearer, more intuitive and informative installer. It also creates a file to facilitate user support.

  • Refactored the deep learning toolkit, more robust and new environment with updated tensorflow.

  • Updated requirement.

More Xmipp

  • Added half precission suport to numpy

  • Added the ability to read and write CIF files

  • Modular design of winner filter

  • Decoupling XmippTomo from XmippSPA

  • Fix Zernike equation - Removed all occurrences of non base-class default destructors

  • Improved MultidimArray performance

  • Added support for half precision floating point numbers in MRCs

  • Assign tiff to gain files - adding half maps labels

3.23.03 - Kratos

Xmipp Programs

  • New programs: tomo_confidence_map, tomo_extract_particlestacks, tomo_extract_subtomograms, tomo_tiltseries_dose_filter, psd_estimatator

  • Deprecated programs (for more details visit the wiki): angular_distribution_show, apropos ctf_correct_idr, ctf_create_ctfdat , ctf_show , idr_xray_tomo , image_common_lines , metadata_convert_to_spider , metadata_selfile_create , mlf_refine_3d, ml_refine_3d, ml_tomo , mrc_create_metadata , pdb_construct_dictionary, pdb_restore_with_dictionary , reconstruct_admn , reconstruct_art_pseudo , resolution_ibw , resolution_ssnr , score_micrograph , reconstruct_fourier_starpu , tomo_align_tilt_series, tomo_align_dual_tilt_series, tomo_align_refinement, tomo_align_refinement, tomo_extract_subvolume, tomo_project_main, tomo_remove_fluctuations , tomo_align_tilt_series,transform_range_adjust , validation_tilt_pairs , volume_pca , volume_validate_pca , work_test , 6f4d983 , evaulate_coordinates , extract_subset , image_separate_objects , volume_enhance_contrast , volume_reslice , xray_import , xray_project , xray_psf_create , xray_reconstruct_art , gpu_correlation, gpu_utils, classify_significant, deepAlign.

  • volume_from_pdb: fixing input pdb file being overwritten when β€˜-centerPDB’ flag was set

  • xmipp_phantom_movie: adding support for fixed step shift & gain and dark image generation

  • CTF simulation allows astigmatism

  • xmipp_metadata_utility: Now join operations with an empty set will return a new empty set (previously no output file was generated).

  • xmipp_matrix_dimred: Program help improved. Exception is now thrown when the number of output dimensions is larger than the input dimensions

  • xmipp_angular_distance: Added itemId column to the output

Installation and user guide

  • Refactor and simplified Readme page.

  • Updating CUDA version compatibility

  • Updating gcc version availables

  • Fixed Matlab installation

  • Added missing array include to fix compilation error with g++12

  • Alert and not block compilation if gcc

  • CUDA are not compatible

  • Avoid compilation warnings

  • Required pyworkflow==3.0.31

Others

  • Maintenance: Recovered python binding tests

  • Maintenance: fixing dangling pointer in xmipp_error

  • Maintenance: Cleaned includes in xmipp_image_base

  • PSD estimation: templating function, improving performance

  • Flag cleanDeprecate in the installation; clean all deprecated executables programs

  • python binding: fixed bug when Numpy arrays created by slicing were badly interpretted - Removed β€œseed” library

  • Fixed memory pinning CUDA bug - Fixed compilation errors on CUDA 9

3.22.11 - Iris

Xmipp Programs

  • Speeding up iterations in some xmipp programs (xmipp_ctf_group, xmipp_image_histogram, xmipp_mpi_angular_class_average, xmipp_angular_distance, xmipp_angular_estimate_tilt_axis, xmipp_ctf_create_ctfdat, xmipp_resolution_ssnr)

  • New Zernike3D programs

  • angular_project_library: Reported some error if there are no images in the range

  • angular_discrete_assign.cpp: Removed memory leak and uninitialized values

  • angular_distance: Fixing condition to avoid iteration behind the end of the MD in cases when input data have different sizes. Optimized performance

  • Pdb_reduce_pseudoatoms: Produced pdb is one-based indexed - xmipp_micrograph_automatic_picking: Fixing memory leak

  • subtract_projection: Fixed several bugs (improved results), added circular mask to avoid edge artifacts, added option to boost particles instead of subtract

Installation and user guide

  • Various bug fixing

  • More information about hdf5 library

  • Updating CUDA

  • GCC compatibility. Added CUDA 11.7 (not tested)

  • Updating Readme

Others

  • Performance optimization (metadata binding)

  • Python binding: adding methods to directly set / get entire MD row

  • g++ >= 8 required

  • In viewers used pwutils

  • The pdb data library now has all the right fields and should write the record type (β€œATOM” or β€œHETATM”) correctly at the beginning of the line and the atomType (element) and charge (if applicable) correctly at the end of the line.

  • Removal of anartifact of symmetrization related to the z pitch (symmetries.cpp)

  • Using the same identical Deprecated param from pyworkflow.

3.22.07 - Helios

Scripts Xmipp

  • xmipp_image_operate: taked into account non existing files

  • angular_continuous_assign2: Bug fixed

  • volume_consensus: Bug fixed

  • ctf.h and angular_continuous_assign_2: Changes for local defocus estimation #578

Installation and user guide

  • Version info printed at the end of the installation

  • Removed empty folder with cleanBin command

  • Clarifing linking to Scipion and removed a bug with the build link

  • New flag (OPENCV_VERSION) in xmipp.config

  • Updated Readme (explain OpenCV-CUDA support)

Others

  • Validation server: Merged what remains

  • Replaced sincos to sin and cos

  • Handling of pointers in MPI programs

  • β€œnullptr” used to denote the null pointer not β€œNULL”

  • Check if nvidiaDriverVer is None

3.22.04 - Gaia

Installation and user guide

  • Updated readme

  • Updated hdf5 info troubleshoting

  • Updated Standalone installation

  • Updated Scons installation

  • xmipp get_models: fixing the run and download path

  • Updating xmipp links for Scipion on installation

  • Removed fatal message in installation

  • Reported error if happen on installation - runjob

  • Ensuring that target directory for the libraries exists

Protocols scipion-em-xmipp

  • protocol_core_analysis: New protocol

  • protocol_compare_angles: Bug fix in compare angles under some conditions

  • protocol_center_particles: protocol simplified (removed setofCoordinates as output)

  • protocol_CTF_consensus: concurrency error fixed

  • protocol_convert_pdb: remove size if deactivated

  • protocol_resolution_deepres: binary masked not stored in Extra folder and avoiding memory problems on GPUs

  • protocol_add_noise: fixes

  • protocol_compare_reprojections: improve computation of residuals + tests + fix + formatting

  • protocol_screen_deepConsensus: multiple fixes in batch processing, trainging and streaming mode

  • protocol_shift_particles: apply transform is now optional

Others

  • New XMIPP logo

  • subtract_projection: adding new flag + fix

  • Add intersection size metadata (bindings/python)

  • Fixed unitialized unique pointers (bindings/python)

  • Bug fixing: Resolution directional and anisotropic filtering fixing the test

  • Removed SonarCloud issues

  • Replaced defines with constexpr

  • Removing Unused funtion parameters

  • Division by zero

  • Memory management

  • Removed field shadowing

  • Destructors should not throw exceptions

3.22.01 - Eris

  • Updating to C++17

  • Support newer versions of CUDA and gcc

  • Zernike programs compatible with Cuda 8.x

  • Fixed Sonar Cloud issues and bugs

  • Matlab compilation Fixed

  • Fixed importing pwem.metadata

  • nma_alignment: Fixed arguments for the xmipp_angular_projection_matching invocation

  • Fixed test fails: ResolutionSsnr, ReconstructArtMpi, ReconstructArt, MlfRefine3dMpi, MlfRefine3d, MlRefine3dMpi, MlRefine3d, xmipp_test_pocs_main & volume_subtraction

  • xmipp_micrograph_automatic_picking: Fixed tests, avoid possible memory corruption

  • resolution_pdb_bfactor: bug fixed - error with multiple chains

  • FlexAlign: Fixed crash when binning > 1

  • Bug fixed and allowed controlling high sampling rate

  • Volume consensus: Fixed number of levels in the wavelet transform

  • Compilation: Fixed compilation of starpu programs

  • xmipp_transform_dimred: Fixed output metadata in append mode, adding MDL_DIMRED label

  • Config file generation: Fixed config version detection outside of the git repo, refactored check_CUDA and managed gcc compiler if it is installed out of /usr/bin/, check and exit if xmipp.conf does not exist

  • Compilation: Fixed detection of the last commit changed the config script

  • Resolution_fso: Bingham test implemented

  • Opencv not detected. Added include to user/include/opencv4 folder on config file

  • Compilation: asking whether to continue with compilation even though the config file is outdated

  • XMIPP install: Linked libsvm to scipion

  • Installation: Referenced β€˜global’ xmipp.conf instead of using local copy of it

  • Multiple MPI programs: replaced CREATE_MPI_METADATA_PROGRAM macro by templated class

  • python_constants: add defocus labels

  • Metadata: added new nmaEigenval label

  • Python binding: added new function - correlationAfterAlignment, MDL_RESOLUTION_ANISOTROPY, MDL_RESOLUTION_ANISOTROPY

  • Matlab binding dependencies: set XMIPP as a hard dependency

  • Projections subtraction: new program

  • FFTwT: added mutex for plan handling

  • Multiple programs: Added a common implementation of the rerun

  • Phantom_create: update info link

  • Multiple programs: Added a common implementation of the rerun

  • Transform Geometry: save new shifted coordinates in option β€œshift to” + enterOfMass to python binding

  • Readme info: add virtual machine info

  • Removal of the SVM from inside the XMIPP repository and downloading it as an external dependence

  • Solved a configuration problem with CUDA

  • ml_tomo: Using .mrc instead of .vol ; volume_align: Addded wrapping during alignment

3.21.06 - Caerus

  • CUDA-11 support

  • New protocol: Deep align

  • ChimeraX support

  • Improvements of streaming process

  • Several performance optimizations

  • Build time optimization

  • Multiple bug fixes

  • Improved documentation

3.20.07 - Boreas

  • Fast CTF estimation

  • CTF includes phase shifts now

  • Selection of alpha helices or beta sheets from a PDB (xmipp_pdb_select)

  • Centering a PDB (xmipp_pdb_center)

  • New Protocol: MicrographCleaner is a new algorithm that removes coordinates picked from carbon edges, aggregations, ice crystals and other contaminations

  • New functionality: The protocol compare reprojections can now compute the residuals after alignment

  • New protocol: Split frames divide input movies into odd and even movies so that they can be processed independently

  • New protocol: Continuous heterogeneity analysis using spherical harmonics (not ready to be used)

  • Bug fixing when some micrograph has no coordinates in the consensus-picking.

  • New functionalities: Different architectures and training modes

  • Normal Mode Analysis protocols have been moved to the plugin ContinuousFlex

  • Fixing MPI version of the Fourier Reconstruction

  • New protocol: local CTF integration and consensus protocol for local ctf (also the viewers)

  • Local CTF analysis tools: Not yet ready for general public

  • New functionallity: Introducing the posibility of automatic estimation of the gain orientation.

  • Bugs fixings regarding stability on streaming processing

  • Support of heterogeneous movie sets

  • New protocol: Clustering of subtomogram coordinates into connected components that can be processed independently

  • New Protocol: Removing duplicated coordinates

  • New protocol: Subtomograms can be projected in several ways to 2D images so that 2D clustering tools can be used

  • New protocol: Regions of Interest can be defined in tomograms (e.g., membranes)

  • Bug fixing in mask3d protocol

  • Bug fix: in helical search symmetry protocol

  • Enhanced precision of the FlexAlign program

  • Now, deepLearningToolkit is under its own conda environment

  • Multiple protocols accelerated using GPU

  • New functionality: Xmipp CTF estimation can now take a previous defocus and do not change it

  • New functionallity: CTF-consensus is able to take the primary main values or an average of the two.

  • New functionallity: CTF-consensus is able to append metadata from the secondary input

  • New functionality: Xmipp Highres can now work with non-phase flipped images

  • New functionality: Xmipp Preprocess particles can now phase flip the images

  • New protocol: Tool to evaluate the quality of a map-model fitting

  • Allowing multi-GPU processing using FlexAlign

  • Improvement in monores and localdeblur

  • Randomize phases also available for images

  • Change the plugin to the new Scipion structure

  • Migrating the code to python3