All modules for which code is available

• pwem
• pwem.convert.atom_struct
• pwem.convert.headers
• pwem.convert.sequence
• pwem.convert.symmetry
• pwem.convert.trigonometry
• pwem.convert.utils
• pwem.emlib.image.image_handler
• pwem.emlib.image.image_readers
• pwem.emlib.metadata.utils
• pwem.objects.data
• pwem.objects.data_flexhub
• pwem.objects.data_tiltpairs
• pwem.protocols.parallel
• pwem.protocols.protocol
• pwem.protocols.protocol_2d
• pwem.protocols.protocol_3d
• pwem.protocols.protocol_align_movies
• pwem.protocols.protocol_alignment_assign
• pwem.protocols.protocol_alignment_invertHand
• pwem.protocols.protocol_base_flexhub
• pwem.protocols.protocol_batch
• pwem.protocols.protocol_boxsize_checkpoint
• pwem.protocols.protocol_boxsize_parameters
• pwem.protocols.protocol_classes_selector
• pwem.protocols.protocol_create_stream_data
• pwem.protocols.protocol_ctf_assign
• pwem.protocols.protocol_export.protocol_export_DB
• pwem.protocols.protocol_extract_coordinates
• pwem.protocols.protocol_import.base
• pwem.protocols.protocol_import.coordinates
• pwem.protocols.protocol_import.ctfs
• pwem.protocols.protocol_import.dataimport
• pwem.protocols.protocol_import.images
• pwem.protocols.protocol_import.masks
• pwem.protocols.protocol_import.micrographs
• pwem.protocols.protocol_import.particles
• pwem.protocols.protocol_import.sequence
• pwem.protocols.protocol_import.volumes
• pwem.protocols.protocol_mathematical_operator
• pwem.protocols.protocol_micrographs
• pwem.protocols.protocol_movie_eraser
• pwem.protocols.protocol_movies
• pwem.protocols.protocol_origin_sampling_volume
• pwem.protocols.protocol_particles
• pwem.protocols.protocol_particles_picking
• pwem.protocols.protocol_pdf_report
• pwem.protocols.protocol_projection_edit
• pwem.protocols.protocol_set_editor
• pwem.protocols.protocol_set_filter
• pwem.protocols.protocol_sets
• pwem.protocols.protocol_tests
• pwem.protocols.protocol_tiltpairs
• pwem.protocols.protocol_tools
• pwem.protocols.protocol_wait
• pwem.utils
• pwem.viewers.filehandlers
• pwem.viewers.plotter
• pwem.viewers.showj
• pwem.viewers.viewer_angular_dist
• pwem.viewers.viewer_base
• pwem.viewers.viewer_chimera
• pwem.viewers.viewer_coordinates
• pwem.viewers.viewer_fsc
• pwem.viewers.viewer_localres
• pwem.viewers.viewer_pdf
• pwem.viewers.viewer_sequence
• pwem.viewers.viewer_vmd
• pwem.viewers.viewer_volumes
• pwem.viewers.viewers_data
• pwem.viewers.views
• pwem.wizards.wizard
• pwem.wizards.wizards
• pwem.wizards.wizards_3d.callbacks
• pwem.wizards.wizards_3d.mask_structure_wizard
• pwem.wizards.wizards_3d.mask_volume_wizard
• pyworkflow.apps.pw_plot
• pyworkflow.apps.pw_project
• pyworkflow.apps.pw_protocol_list
• pyworkflow.apps.pw_run_tests
• pyworkflow.apps.pw_schedule_run
• pyworkflow.apps.pw_sync_data
• pyworkflow.apps.pw_viewer
• pyworkflow.config
• pyworkflow.constants
• pyworkflow.exceptions
• pyworkflow.gui.browser
• pyworkflow.gui.canvas
• pyworkflow.gui.dialog
• pyworkflow.gui.form
• pyworkflow.gui.graph
• pyworkflow.gui.graph_layout
• pyworkflow.gui.gui
• pyworkflow.gui.matplotlib_image
• pyworkflow.gui.plotter
• pyworkflow.gui.project.base
• pyworkflow.gui.project.labels
• pyworkflow.gui.project.project
• pyworkflow.gui.project.searchprotocol
• pyworkflow.gui.project.searchrun
• pyworkflow.gui.project.steps
• pyworkflow.gui.project.utils
• pyworkflow.gui.project.variables
• pyworkflow.gui.project.viewdata
• pyworkflow.gui.project.viewprojects
• pyworkflow.gui.project.viewprotocols
• pyworkflow.gui.project.viewprotocols_extra
• pyworkflow.gui.text
• pyworkflow.gui.tooltip
• pyworkflow.gui.tree
• pyworkflow.gui.widgets
• pyworkflow.mapper.mapper
• pyworkflow.mapper.sqlite
• pyworkflow.mapper.sqlite_db
• pyworkflow.object
• pyworkflow.plugin
• pyworkflow.project.config
• pyworkflow.project.manager
• pyworkflow.project.project
• pyworkflow.protocol.executor
• pyworkflow.protocol.hosts
• pyworkflow.protocol.launch
• pyworkflow.protocol.package
• pyworkflow.protocol.params
• pyworkflow.protocol.protocol
• pyworkflow.template
• pyworkflow.tests.test_utils
• pyworkflow.tests.tests
• pyworkflow.utils.dataset
• pyworkflow.utils.echo
• pyworkflow.utils.graph
• pyworkflow.utils.log
• pyworkflow.utils.path
• pyworkflow.utils.process
• pyworkflow.utils.profiler
• pyworkflow.utils.progressbar
• pyworkflow.utils.properties
• pyworkflow.utils.reflection
• pyworkflow.utils.utils
• pyworkflow.utils.which
• pyworkflow.viewer
• pyworkflow.webservices.notifier
• pyworkflow.webservices.repository
• pyworkflow.webservices.workflowhub
• pyworkflow.wizard
• scipion.guiplugin
• scipion.install.change_rpath
• scipion.install.clean
• scipion.install.find_deps
• scipion.install.funcs
• scipion.install.inspect_plugins
• scipion.install.install_plugin
• scipion.install.plugin_funcs
• scipion.install.plugin_manager
• scipion.install.update_manager
• scipion.scripts.config
• scipion.scripts.fontbrowser
• scipion.scripts.kickoff
• scipion.scripts.tutorial
• scipion.utils
• xmipp3
• xmipp3.base
• xmipp3.convert.convert
• xmipp3.convert.dataimport
• xmipp3.convert.io_coordinates
• xmipp3.programs
• xmipp3.protocols.protocol_align_volume
• xmipp3.protocols.protocol_align_volume_and_particles
• xmipp3.protocols.protocol_analyze_local_ctf
• xmipp3.protocols.protocol_angular_graph_consistency
• xmipp3.protocols.protocol_angular_resolution_alignment
• xmipp3.protocols.protocol_apply_alignment
• xmipp3.protocols.protocol_apply_tilt_to_ctf
• xmipp3.protocols.protocol_apply_transformation_matrix
• xmipp3.protocols.protocol_apply_zernike3d
• xmipp3.protocols.protocol_assignment_tilt_pair
• xmipp3.protocols.protocol_break_symmetry
• xmipp3.protocols.protocol_center_particles
• xmipp3.protocols.protocol_cl2d
• xmipp3.protocols.protocol_cl2d_align
• xmipp3.protocols.protocol_classes_2d_mapping
• xmipp3.protocols.protocol_classify_pca
• xmipp3.protocols.protocol_classify_pca_streaming
• xmipp3.protocols.protocol_compare_angles
• xmipp3.protocols.protocol_compare_reprojections
• xmipp3.protocols.protocol_consensus_classes
• xmipp3.protocols.protocol_consensus_local_ctf
• xmipp3.protocols.protocol_convert_pdb
• xmipp3.protocols.protocol_core_analysis
• xmipp3.protocols.protocol_create_gallery
• xmipp3.protocols.protocol_ctf_consensus
• xmipp3.protocols.protocol_ctf_correct_wiener2d
• xmipp3.protocols.protocol_ctf_defocus_group
• xmipp3.protocols.protocol_ctf_micrographs
• xmipp3.protocols.protocol_deep_center
• xmipp3.protocols.protocol_deep_hand
• xmipp3.protocols.protocol_deep_micrograph_screen
• xmipp3.protocols.protocol_denoise_particles
• xmipp3.protocols.protocol_eliminate_empty_images
• xmipp3.protocols.protocol_enrich
• xmipp3.protocols.protocol_extract_asymmetric_unit
• xmipp3.protocols.protocol_extract_particles
• xmipp3.protocols.protocol_extract_particles_movies
• xmipp3.protocols.protocol_extract_particles_pairs
• xmipp3.protocols.protocol_flexalign
• xmipp3.protocols.protocol_generate_reprojections
• xmipp3.protocols.protocol_helical_parameters
• xmipp3.protocols.protocol_kerdensom
• xmipp3.protocols.protocol_local_ctf
• xmipp3.protocols.protocol_ml2d
• xmipp3.protocols.protocol_movie_alignment_consensus
• xmipp3.protocols.protocol_movie_dose_analysis
• xmipp3.protocols.protocol_movie_gain
• xmipp3.protocols.protocol_movie_max_shift
• xmipp3.protocols.protocol_movie_opticalflow
• xmipp3.protocols.protocol_movie_split_frames
• xmipp3.protocols.protocol_multiple_fscs
• xmipp3.protocols.protocol_multireference_alignability
• xmipp3.protocols.protocol_normalize_strain
• xmipp3.protocols.protocol_particle_pick
• xmipp3.protocols.protocol_particle_pick_automatic
• xmipp3.protocols.protocol_particle_pick_consensus
• xmipp3.protocols.protocol_particle_pick_pairs
• xmipp3.protocols.protocol_particle_pick_remove_duplicates
• xmipp3.protocols.protocol_phantom_create
• xmipp3.protocols.protocol_pick_noise
• xmipp3.protocols.protocol_postProcessing_deepPostProcessing
• xmipp3.protocols.protocol_preprocess.geometrical_mask
• xmipp3.protocols.protocol_preprocess.protocol_add_noise
• xmipp3.protocols.protocol_preprocess.protocol_create_mask2d
• xmipp3.protocols.protocol_preprocess.protocol_create_mask3d
• xmipp3.protocols.protocol_preprocess.protocol_crop_resize
• xmipp3.protocols.protocol_preprocess.protocol_filter
• xmipp3.protocols.protocol_preprocess.protocol_image_operate
• xmipp3.protocols.protocol_preprocess.protocol_mask
• xmipp3.protocols.protocol_preprocess.protocol_movie_resize
• xmipp3.protocols.protocol_preprocess.protocol_preprocess
• xmipp3.protocols.protocol_preprocess.protocol_process
• xmipp3.protocols.protocol_preprocess_micrographs
• xmipp3.protocols.protocol_projmatch.projmatch_initialize
• xmipp3.protocols.protocol_projmatch.projmatch_steps
• xmipp3.protocols.protocol_projmatch.protocol_projmatch
• xmipp3.protocols.protocol_random_conical_tilt
• xmipp3.protocols.protocol_ransac
• xmipp3.protocols.protocol_reconstruct_fourier
• xmipp3.protocols.protocol_reconstruct_highres
• xmipp3.protocols.protocol_reconstruct_significant
• xmipp3.protocols.protocol_reconstruct_swarm
• xmipp3.protocols.protocol_resolution3d
• xmipp3.protocols.protocol_resolution_bfactor
• xmipp3.protocols.protocol_resolution_deepres
• xmipp3.protocols.protocol_resolution_directional
• xmipp3.protocols.protocol_resolution_fso
• xmipp3.protocols.protocol_resolution_monogenic_signal
• xmipp3.protocols.protocol_rotate_volume
• xmipp3.protocols.protocol_rotational_symmetry
• xmipp3.protocols.protocol_screen_deepConsensus
• xmipp3.protocols.protocol_screen_deeplearning
• xmipp3.protocols.protocol_screen_particles
• xmipp3.protocols.protocol_shift_particles
• xmipp3.protocols.protocol_shift_volume
• xmipp3.protocols.protocol_simulate_ctf
• xmipp3.protocols.protocol_structure_map
• xmipp3.protocols.protocol_structure_map_zernike3d
• xmipp3.protocols.protocol_subtract_projection
• xmipp3.protocols.protocol_tilt_analysis
• xmipp3.protocols.protocol_trigger_data
• xmipp3.protocols.protocol_validate_fscq
• xmipp3.protocols.protocol_validate_nontilt
• xmipp3.protocols.protocol_validate_overfitting
• xmipp3.protocols.protocol_volume_adjust_sub
• xmipp3.protocols.protocol_volume_consensus
• xmipp3.protocols.protocol_volume_deform_zernike3d
• xmipp3.protocols.protocol_volume_local_adjust
• xmipp3.protocols.protocol_volume_local_sharpening
• xmipp3.protocols.protocol_volume_strain
• xmipp3.protocols.protocol_write_testC
• xmipp3.protocols.protocol_write_testP
• xmipp3.utils
• xmipp3.viewers.plotter
• xmipp3.viewers.viewer
• xmipp3.viewers.viewer_analyze_local_ctf
• xmipp3.viewers.viewer_angular_resolution_alignment
• xmipp3.viewers.viewer_apply_tilt_to_ctf
• xmipp3.viewers.viewer_cl2d
• xmipp3.viewers.viewer_consensus_classes
• xmipp3.viewers.viewer_ctf_consensus
• xmipp3.viewers.viewer_deepEMHancer
• xmipp3.viewers.viewer_deep_consensus
• xmipp3.viewers.viewer_deep_micrograph_cleaner
• xmipp3.viewers.viewer_dose_analysis
• xmipp3.viewers.viewer_eliminate_empty_images
• xmipp3.viewers.viewer_extract_asymmetric_unit
• xmipp3.viewers.viewer_local_sharpening
• xmipp3.viewers.viewer_ml2d
• xmipp3.viewers.viewer_movie_alignment
• xmipp3.viewers.viewer_normalize_strain
• xmipp3.viewers.viewer_pdb_deform_zernike3d
• xmipp3.viewers.viewer_projmatch
• xmipp3.viewers.viewer_ransac
• xmipp3.viewers.viewer_reconstruct_highres
• xmipp3.viewers.viewer_resolution3d
• xmipp3.viewers.viewer_resolution_bfactor
• xmipp3.viewers.viewer_resolution_deepres
• xmipp3.viewers.viewer_resolution_directional
• xmipp3.viewers.viewer_resolution_fso
• xmipp3.viewers.viewer_resolution_monogenic_signal
• xmipp3.viewers.viewer_structure_map
• xmipp3.viewers.viewer_subtract_projection
• xmipp3.viewers.viewer_swarm
• xmipp3.viewers.viewer_validate_fscq
• xmipp3.viewers.viewer_validate_nontilt
• xmipp3.viewers.viewer_validate_overfitting
• xmipp3.viewers.viewer_volume_consensus
• xmipp3.viewers.viewer_volume_deform_zernike3d
• xmipp3.viewers.viewer_volume_strain
• xmipp3.viewers.viewer_volume_subtraction
• xmipp3.wizards