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.

Prediction:

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

\

--cryolo_predict_path

crYOLO predict executeable

Path to the crYOLO prediction executeable (default none)

config_path

Config file: Path of the crYOLO config file. (default required)

target_dir

Image directory

Folder which contain all images. (default none)

model_path

Model path

Path to the trained model. (default required)

output_dir

Output directory

Folder to write the box files. (default none)

--confidence_threshold

Confidence threshold [0-1]

Confidence threshold for picking. Particles with a confidence threshold lower than this value will be discarded. (default 0.3)

--gpu

GPUs

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

Filament mode [True/False]

Check if you want to use the filament mode. (default False)

--filament_width

Filament width [Pixel]

Width of your filament in pixel. (default 100)

--filament_mode==True

--min_box_per_filament

Minimum number of boxes per filament

Specifies the minimum number of boxes per filament. (default 6)

--filament_mode==True

--box_distance

Box distance

Distance between two boxes in pixel. (default 20)

--filament_mode==True

--nosplit: Don't split curved filaments

If checked, the filament mode does not split to curved filaments. (default False)

--filament_mode==True

--nomerging: Don't merge filaments

If checked, the filament mode does not merge filaments. (default False)

--filament_mode==True

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

Write box and star files into the output directory

See the reference below.

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

• Initial creation of the document

https://doi.org/10.1101/356584

Thorsten Wagner

Category 1:: APPLICATIONS

sparx/bin/sp_cryolo_predict.py

crYOLO

Stable

None right now.