prediction command for crYOLO.
Tags
templatejavaimagej2scijava
Citation
Wagner, T., Merino, F., Stabrin, M., Moriya, T., Antoni, C., Apelbaum, A., Hagel, P., Sitsel, O., Raisch, T., Prumbaum, D. and Quentin, D., 2019. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Communications biology, 2(1), p.218..https://cryolo.readthedocs.io/en/stable/index.html
Solution written by
Kyle Harrington
License of solution
MIT
Arguments
--conf
Path to the crYOLO configuration file. (default value: PARAMETER_VALUE)
--weights
Path to the trained model. (default value: PARAMETER_VALUE)
--input
Path to one or multiple image folders/images. (default value: PARAMETER_VALUE)
--output
Path to the output folder. (default value: PARAMETER_VALUE)
--threshold
Confidence threshold. (default value: PARAMETER_VALUE)
--gpu
Specify which GPU(s) should be used. (default value: PARAMETER_VALUE)
--distance
Distance for particle removal. (default value: PARAMETER_VALUE)
--minsize
Minimum estimated diameter for particles. (default value: PARAMETER_VALUE)
--maxsize
Maximum estimated diameter for particles. (default value: PARAMETER_VALUE)
--prediction_batch_size
Number of images predicted in one batch. (default value: PARAMETER_VALUE)
--gpu_fraction
Fraction of memory per GPU used during prediction. (default value: PARAMETER_VALUE)
--num_cpu
Number of CPUs used during filtering/filament tracing. (default value: PARAMETER_VALUE)
--norm_margin
Relative margin size for normalization. (default value: PARAMETER_VALUE)
--monitor
Activate monitoring mode for input folder. (default value: PARAMETER_VALUE)
--otf
On the fly filtering, filtered micrographs will not be written to disk. (default value: PARAMETER_VALUE)
--cleanup
Delete filtered images after prediction is done. (default value: PARAMETER_VALUE)
--skip
Skip images that were already picked. (default value: PARAMETER_VALUE)
--filament
Activate filament mode. (default value: PARAMETER_VALUE)
--box_distance
Distance in pixel between two boxes. (default value: PARAMETER_VALUE)
--minimum_number_boxes
Minimum number of boxes per filament. (default value: PARAMETER_VALUE)
--straightness_method
Method to measure the straightness of a line. (default value: PARAMETER_VALUE)
--straightness_threshold
Threshold value for the straightness method. (default value: PARAMETER_VALUE)
--search_range_factor
The search range for connecting boxes. (default value: PARAMETER_VALUE)
--angle_delta
Angle delta in degree. (default value: PARAMETER_VALUE)
--directional_method
Method for directional filament estimation. (default value: PARAMETER_VALUE)
--filament_width
Filament width in pixel. (default value: PARAMETER_VALUE)
--mask_width
Mask width in pixel for convolution method. (default value: PARAMETER_VALUE)
--nosplit
(DEPRECATED) Do not split to curved filaments. (default value: PARAMETER_VALUE)
--nomerging
Do not merge filaments. (default value: PARAMETER_VALUE)
--tomogram
Activate tomography picking mode. (default value: PARAMETER_VALUE)
--tracing_search_range
Search range in pixel for tracing. (default value: PARAMETER_VALUE)
--tracing_memory
Tracing memory in frames for particle tracking. (default value: PARAMETER_VALUE)
--minimum_number_boxes_3d
Minimum number of boxes per filament in 3D mode. (default value: PARAMETER_VALUE)
--tracing_min_length
Minimum number of boxes in one trace for valid particle. (default value: PARAMETER_VALUE)
--tracing_window_size
Window width when averaging filament positions. (default value: PARAMETER_VALUE)
--tracing_min_edge_weight
Minimum edge weight for filament tracing. (default value: PARAMETER_VALUE)
--tracing_merge_thresh
Threshold for merging filaments in tracing. (default value: PARAMETER_VALUE)
--patch
(DEPRECATED) Number of patches. (default value: PARAMETER_VALUE)
--write_empty
Write empty box files when no particle could be found. (default value: PARAMETER_VALUE)