This version (2019/04/02 11:40) is a draft.
Approvals: 0/1

crYOLO - predict: Prediction with crYOLO, a deep learning high accuracy particle picking procedure.

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 --nomerging

To pick with crYOLO one have to specifiy the config file, the target folder containing the images and the output folder for writing the box files. Optionally one can specify the confidence threshold and which GPUs should be used.


sp_cryolo_predict.py config_path target_dir model_path output_dir --confidence_threshold=0.3 --gpu=0


Main Parameters

crYOLO predict executeable
Path to the crYOLO prediction executeable (default none)
Config file: Path of the crYOLO config file. (default required)
Image directory
Folder which contain all images. (default none)
Model path
Path to the trained model. (default required)
Output directory
Folder to write the box files. (default none)

Advanced Parameters

Confidence threshold [0-1]
Confidence threshold for picking. Particles with a confidence threshold lower than this value will be discarded. (default 0.3)
List of GPUs to use. (default 0)
--gpu_fraction: GPU memory fraction
Specify the fraction of memory per GPU used by crYOLO during prediction. Only values between 0.0 and 1.0 are allowed. (default 1.0)
--num_cpu: Number of CPUs
Number of CPUs used during prediction. By default it will use half of the available CPUs. (default 1.0)
Filament mode [True/False]
Check if you want to use the filament mode. (default False)
Filament width [Pixel]
Width of your filament in pixel. (default 100)
Minimum number of boxes per filament
Specifies the minimum number of boxes per filament. (default 6)
Box distance
Distance between two boxes in pixel. (default 20)
--nosplit: Don't split curved filaments
If checked, the filament mode does not split to curved filaments. (default False)
--nomerging: Don't merge filaments
If checked, the filament mode does not merge filaments. (default False)

It will write box and star files into your output directory.

List of Output Files

Write box and star files into the output directory

See the reference below.

Picking is very fast with up to 8 micrographs / s.

2019/09/24 Thorsten Wagner

  • Initial creation of the document

Thorsten Wagner




None right now.

  • pipeline/window/sp_cryolo_predict.txt
  • Last modified: 2019/04/02 11:40
  • by lusnig