https://sphire.mpg.de/wiki/ 2026-05-01T02:33:06+00:00 https://sphire.mpg.de/wiki/ https://sphire.mpg.de/wiki/lib/tpl/dokuwiki/images/favicon.ico text/html 2021-02-19T10:00:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:window:cryolo&rev=1613725208&do=diff Overview NEW DOCUMENTATION https://cryolo.readthedocs.io CrYOLO is a fast and accurate particle picking procedure. It's based on convolutional neural networks and utilizes the popular You Only Look Once (YOLO) object detection system. * crYOLO makes picking fast – On a modern GPU it will pick your particles at up to 6 micrographs per second. text/html 2019-04-02T09:21:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:window:e2boxer&rev=1554189686&do=diff e2boxer Particle Coordinates (NEW): Generate files containing particle coordinates for all input micrographs by picking particles manual and/or automatically. Usage Usage in command line e2boxer.py input_micrograph_list --apix=PIXEL_SIZE --boxsize=BOX_SIZE --ptclsize=PARTICLE_DIAMETER --invert --no_ctf --gui --write_dbbox --allmicrographs --unboxedonly --write_ptcls --suffix=SUFFIX --voltage=VOLTAGE --cs=CS --ac=AMP_CONTRAST --autopick=MODE --threads=THREADS --ppid=PPID … text/html 2019-04-02T09:12:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:window:e2boxer_old&rev=1554189143&do=diff e2boxer_old Particle Coordinates: Generate files containing particle coordinates for all input micrographs by picking particles manual and/or automatically. Usage Usage in command line e2boxer_old.py input_micrograph_list --boxsize=BOXSIZE --write_dbbox --write_ptcls --exclude_edges --force --format=FORMAT --norm=NORM --invert --suffix=SUFFIX --dbls=DBLS --autoboxer=AUTOBOXER --ppid=PPID --gui --verbose=n --gauss_autoboxer=GAUSS_AUTOBOXER --do_ctf=DO_CTF --cter --indir=I… text/html 2019-04-02T11:41:36+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:window:sp_cryolo_boxmanager&rev=1554198096&do=diff sp_cryolo_boxmanager crYOLO - boxmanager: Displays boxfiles on images. Allows creation of new training data for crYOLO. Usage Usage in command line sp_cryolo_boxmanager.py --target_dir=target_dir --box_dir=box_dir Typical usage 1. Open images sp_cryolo_boxmanager.py images_dir text/html 2019-04-02T11:40:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:window:sp_cryolo_predict&rev=1554198025&do=diff sp_cryolo_predict crYOLO - predict: Prediction with crYOLO, a deep learning high accuracy particle picking procedure. Usage Usage in command line sp_cryolo_predict.py config_path target_dir model_path output_dir --cryolo_predict_path=CRYOLO_PATH --confidence_threshold=confidence_threshold --gpu=gpu --gpu=GPU_NUMBER --filament_mode --filament_width=FILAMENT_WIDTH --min_box_per_filament=MIN_BOX_PER_FILAMENT --box_distance=BOX_DISTANCE --gpu_fraction=GPU_FRACTION --num_cpu=NUM_CPU --nosplit -… text/html 2019-04-02T11:40:59+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:window:sp_cryolo_train&rev=1554198059&do=diff sp_cryolo_train crYOLO - training: Training of crYOLO, a deep learning high accuracy particle picking procedure. Usage Usage in command line sp_cryolo_train.py particle_diameter training_dir annot_dir --cryolo_train_path=CRYOLO_PATH --architecture=architecture --input_size=input_size --num_patches=num_patches --overlap_patches=overlap_patches --train_times=train_times --pretrained_weights_name=PRETRAINED_NAME --saved_weights_name=SAVE_WEIGHTS_NAME --batch_size=batch_size --learning_rate=le… text/html 2020-05-20T11:44:42+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:window:sp_tilt_import&rev=1589967882&do=diff sp_tilt_import Tilt Import : Imports per-particle defocus estimates from gCTF. Usage Usage in command line: sp_tilt_import.py input_star_files output_directory --box_size=box_size --apix=pixel_size --verbosity=verbosity Typical usage The purpose of sp_tilt_import.py is to: text/html 2019-04-02T11:40:02+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:window:start&rev=1554198002&do=diff WINDOW Commands crYOLO - predict Prediction with crYOLO, a deep learning high accuracy particle picking procedure Particle Extraction Extract particle images from micrographs using particle coordinates files. Particle Stack Combine BDB image stacks of individual micrographs to a single virtual stack of all particles. text/html 2019-04-02T10:32:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:window:sxrewindow&rev=1554193952&do=diff sp_rewindow Particle Reextraction: Rewindow particles from micrographs using the information stored in rebox files. Usage Usage in command line sp_rewindow.py input_micrograph_pattern input_rebox_pattern output_directory --selection_list=SELECTION_TEXT_FILE --box_size=BOX_SIZE --skip_invert --mic_resample_ratio=RATIO --swap_ctf_params=CTER_PARTRES_FILE_PATH --check_consistency text/html 2022-05-25T13:47:03+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:window:sxwindow&rev=1653479223&do=diff sp_window Particle Extraction: Window particles from micrographs using the particle coordinates. Usage Usage in command line sp_window.py input_micrograph_pattern input_coordinates_pattern input_ctf_params_source output_directory --selection_list=SELECTION_TEXT_FILE --coordinates_format=FORMAT_NAME --box_size=SIZE --skip_invert --limit_ctf --astigmatism_error=ERROR_THRESHOLD --resample_ratio=RATIO --check_consistency ---filament_width=FILAMENT_WIDTH