Releases scipion-em-xmipp

3.24.12 - Poseidon

  • New protocols

    • apply_tilt_to_ctf: Apply a local deviation to the CTF based on the micrograph’s tilt angle

    • mics_defocus_balancer: It takes as input a certain number of CTFs and makes a balanced sampling of N images based on the defocus U values

    • deep_center_predict: Center a set of particles in 2D using a neural network

    • cl2d_clustering: 2D clustering protocol to group similar images (2D Averages or 2D Classes)

  • Protocols updated

    • flexalign: Added support for reading EER. Add multi-GPU support. Optimized and refactor the streaming, the continue action stabilized.

    • convert_pdb: now can read cif

    • create_gallery: Allow Scipion protocol create gallery to access missing projection options

    • ctf_consensus: optimized and refactor the streaming, the continue action stabilized. Remove parallelization

    • movie_dose_analysis: optimized and refactor the streaming, the continue action stabilized

    • movie_max_shift: optimized and refactor the streaming, the continue action stabilized, Remove parallelization

    • tilt_analysis: optimized and refactor the streaming, the continue action stabilized

    • subtract_projection: Adaptations for new logic in Xmipp program

    • reconstruct_highres: Add GPU use for local angle assignment

  • Protocols fixed

    • trigger_data: Fix the way we split the output

    • subtract_projection: fnMask sub

    • classify_pca: Bug fix in the validate function

    • reconstruct_fourier: Fourier reconstruction now allows performing the CTF correction inside the same protocol.

    • volume_local_sharpening: local deblur performs now a single iteration by defaul

    • movie_max_shift: fixed with several parallel threads in streaming

    • reconstruct_highres: add unassigned vars fnVol1 fnVol2 to set loop

    • ctf_defocus_group: fix when testing multiple downsampling factors

    • ctf_micrographs: fix when testing multiple downsampling factors

  • Protocols deprecated (For more details visit this)

    • angular_resolution_alignment

    • movie_opticalflow.py

  • More scipion-em-xmipp

    • scikit-learn updated to 1.2

    • protocols.conf list completed. All protocols are listed and clustered in Scipion

3.24.06 - Oceanus

  • New protocols

    • movie_alignment_consensus: protocol for the comparison of two global alignments

    • PCA classification: 2D Classification method that can works in streaming and in static

  • Protocols updated

    • deep_center: Deep center calculates an approximate center for the particles.

    • validate_fscq: Added cif support

    • reconstruct_fourier: Enable reconstructing with halves in the reconstruct fourier

    • simulate_ctf: Simulate CTF can add noise before and after CTF.

    • extract_particles: Local average added

    • compare_reprojections: Downsampling option,autodown sampling, allows input 2D in several formats, allows input 3D in several formats, ranking option available, extraction option available

    • cl2d: ensuring a save classes creating and adding possible output

  • Protocols fixed

    • resolution_deepres:now works with queue system

    • ProcessVolumes: Fix header for resize voxels

    • resolution_bfactor:Fix local resolution to local bfactor

    • resolution_bfactor: create output for res bfac

    • extract_particles: Bug fix in the downsampling factor of extract particles

    • core_analysis: define correctly the particles pointer to have indirect pointer

    • tilt_analysis: estimate automatically the window size new option

    • movie_doseanalysis: update correctly the outputSet

    • extract_particles: Check if resizing is enabled

    • particle_pick_remove_duplicates: Remove duplicates coordinates

  • Protocols deprecated (For more details visit this)

    • deep_denoissing

    • metaprotocol_create_subset

    • metaprotocol_golden_highres

    • solid_angle

    • split_volume

  • More scipion-em-xmipp

    • Solve Sonar Cloud reported bugs

    • Flexible import of pyQT on chimera script

    • Removing tkAgg matplotlib requirement in viewer_structure_map

    • DLTK installation bug local variable and Fix use gpu

    • updated scikit-learn version

    • metaprotocol_golden_highres

    • solid_angle

3.23.11 - Nereus

  • New protocols

    • Volume local adjustment

  • Protocols updated

    • convert_pdb: Allowed conversion natively from CIFs

    • particle_pick_automatic: The model can now be given by a directory

    • volume_local_adjust: Save occupancy volume

    • extract_particles: Added two different cases for downsampling, by dimensions and by sampling rate

  • Protocols fixed

    • movie_resize: Fixed movie resize output size

    • movie_gain: Fix update output step by using a generic one from scipion

    • tilt_analysis: Fixes in the generated tilt images and in updating correctly the output sets

    • ctf_consensus: Fix the dependencies of the step

    • preprocess_micrographs: Fixed output size in preprocess micrographs

    • deep_center_assignment: Fixed deep center calls

    • extract_particles_movies: Get coords correctly

    • particle_pick_consensus: Fix MicsPointer

    • trigger_data: fix updateOutput and close correclty the output set

  • Protocols deprecated (For more details visit this)

    • classification_gpuCorr

    • classification_gpuCorr_full

    • classification_gpuCorr_semi

  • More scipion-em-xmipp

    • Updated Nvidia driver required version

3.23.07 - Morpheus

  • New protocols

    • Movie Dose analysis

    • deep_center

    • deep_global_assignment

    • deep_center_predict

    • deep_global_assignment_predict

  • Protocols updated

    • consensus_classes (Efficient p-value calculation, updated intersection merging process, generalized protocol for other set of classes)

    • Movie Gain: changed _stepsCheckSecs and fixed inputMovies calling, np.asscalar discontinued in numpy 1.16

    • convert_pdb: dont allow set size if template volume, to convert a set of pdbs to volumes, generates an mrc file

    • CTF_consensus: add 4 threads by default

    • process: Better instantiation of Scipion subclasses

    • create_mask3d: Addding a validate in 3dmask, add :mrc to input filename

    • consensus_local_ctf: save defocus in proper fields, compute consensus for local defocus U and V separately, add consensus angle

    • align_volume: Included the label in the volumes

    • crop_resize: Add mask as input. Mask resize is now possible

    • subtract_projection: change pad validation error for warning, parallelized

  • Protocols fixed

    • Tilt analysis: Close correctly the output sets once finished

    • Deep micrograph cleaner: fix two bugs that occured during streaming implementation bug

    • volume_adjust_sub: fix with :mrc

    • Picking consensus: define correctly the possibleOutputs bug

    • Center particles: streaming bug when definining the outputs bug

    • volume_subtraction: bug fixed in filename

    • compare_reprojections: fix update subtract projection output

    • deep_micrograph_screen: Bug fix that prevents using small GPUs

    • consensus_classes:Fixed manual output generation

  • Protocols deprecated (For more details visit this)

    • apply_deformation_zernike3d

    • classify_kmeans2d

    • kmeans_clustering

    • particle_boxSize

    • rotational_spectra

    • split_volume_hierarchical_cluster

  • Viewers

    • viewer_resolution_fs: fixing 0.1 threshold not found

    • viewer_projmatch, viewer_metaprotocol_golden_highres: Fixing viewers, change removed ChimeraClientView to ChimeraView

    • monores_viewer: fix histogram

    • viewer_structure_map: Change the label for each volume

3.23.03 - Kratos

  • New protocol status: beta, new, production and updated. Will appear in the left pannel of Scipion

  • Protocol subtract_projection: user experience improvements, no final mask by default, apply ciruclar mask in adjustment image to avoid edge artifacts, validate same sampling rate with tolerance in third decimal

  • Protocol convert_pdb: Allowed to save centered PDB used for conversion.

  • Protocol align_volume_and_particles: add alingment validation

  • Protocol FlexAlign: updating protocol to reflect changes in the executable, fixed test, removing unused protocol (Movie average)

  • Protocol align_volume_and_particles:Align volume and particles adapted to tomography and works in the absence of tomo plugin.

  • Protocol volume_consensus: validate same sampling rate with tolerance in third decimal

  • Protocols deprecated (for more details visit the wiki): protocol_deep _align, reconstruct_heterogeneous, protocol_metaprotocol_create_output, protocol_metaprotocol_discrete_heterogeneity_scheduler

3.22.11 - Iris

Hot fix 3.22.11.2

  • Align volume and particles works in the absence of tomo plugin.

Hot fix 3.22.11.1

  • Align volume and particles adapted to tomography. Defines possible outputs. Optimized. Test more exhaustive for matrices

3.22.11.0

  • Protocol_cl2d_align: The input can now be a set of averages or a set of 2D classes

  • Protocol_local_ctf: Default value are now changed for maxDefocusChange

  • Protocol_apply_zernike3d: Now accepts either a Volume or SetOfVolumes and applies the coefficients in a loop in the deform step

  • Protocol_postProcessing_deepPostProcessing: Managed GPU memory to avoid errors

  • Protocol_resolution_deepres: Mandatory mask

  • Protocol center particles and Gl2d (all options): Fix streaming

  • Protocol_create_3d_mask: Allows volume Null=True

  • Protocol_reconstruct_fourier: Set pixel size

  • GL2D static: Bug fixing

  • Protocol_trigger_data: Bug fixing

  • Protocol_crop_resize: Set sampling rate of mrc files when cropping resizing volumes or particles

  • subtract_projection: New protocol for boosting particles. Add protocol to wizard XmippParticleMaskRadiusWizard as now the protocol uses it

  • New tests: deep_hand, pick_noise, screen_deep_learning, resolution_B_factor

  • Fixed TestHighres test

3.22.07 - Helios

  • rotate_volume: New protocol

  • subtract_projection: New implementation based on adjustment by regression instead of POCS and improved performance

  • local_ctf: Add new sameDefocus option + formatting

  • compare_reprojections & protocol_align_volume: Fast Fourier by default

  • crop_resize: Allows input pointers

  • resolution_deepres: Resize output to original size

  • denoise_particles: Added setOfAverages as input option

  • process: Change output from stk (spider) to mrcs (mrc)

  • trigger_data: Bug fixed

  • screen_deeplearning: Added descriptive help

  • center_particles: Added summary info

  • align_volume_and_particles: Summary error fixed

  • cl2d: Summary errors solved

  • New tests: test_protocol_reconstruct_fourier, test_protocols_local_defocus, test_protocols_local_defocus, TestXmippAlignVolumeAndParticles, TestXmippRotateVolume

  • Improved tests: test_protocols_deepVolPostprocessing, test_protocols_xmipp_3d, Test ProjSubtracion

  • Excluded tests: test_protocols_zernike3d, test_protocols_metaprotocol_heterogeneity

3.22.04 - Gaia

  • 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

3.22.01 - Eris

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

  • 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

3.19.04

  • Highres can now take a global alignment performed by any other method

  • New protocol: 3D bionotes

  • New protocol: Align volume and particles

  • New protocol: Center particles

  • New protocols: GL2D, GL2D streaming and GL2D static

  • New protocol: 2D kmeans clustering

  • New protocol: compare angles

  • New protocol: consensus 3D classes

  • New protocol: CTF consensus

  • New protocol: deep denoising

  • New protocols: Eliminate empty particles and eliminate empty classes

  • New protocol: Extract unit cell

  • New protocol: Generate reprojections

  • New protocol: metaprotocol heterogenety output, metaprotocol heterogeneity subset and metaprotocol heterogeneity

  • New protocol: Movie Max Shift

  • New protocol: particle boxsize

  • New protocol: pick noise

  • New protocol: significant heterogeneity

  • New protocol: swarm consensus intial volumes

  • New protocol: directional ResDir

  • New protocol: local monoTomo

  • New protocol: deep consensus picking

  • New protocol: screen deep learning

  • New protocol: split volume hierarchical

  • New protocol: trigger data