3.24.06 - Oceanus

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 tom

3.23.11 - Nereus

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.

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

v3.23.03-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 '-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 "seed" library
• Fixed memory pinning CUDA bug
• Fixed compilation errors on CUDA 9