This guide details how to automate the creation, configuration and overall management of a CryoSPARC Live session in Python via the CryoSPARC API.
The instructions are valid for CryoSPARC v3.3.
To run the following commands, you can use the built-in python interpreter provided by CryoSPARC by running cryosparcm icli.
You can also put these functions inside a bash script or a python script. To get access to the CryoSPARC API (cli and rtp) inside a python script, add the following lines to your script, e.g., called automate_cryosparc_live.py:
You will need a project to create your Live session. If you already have a project, you can skip this step.
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'param_name': 'gainref_flip_x',
'param_type': 'boolean',
'base_value': False,
'title': 'Flip gain ref in X?',
'desc': 'Flip gain ref left-to-right (in X axis)'},
{'param_sec': 'mscope_params',
'param_name': 'gainref_flip_y',
'param_type': 'boolean',
'base_value': False,
'title': 'Flip gain ref in Y?',
'desc': 'Flip gain ref top-to-bottom (in Y axis)'},
{'param_sec': 'mscope_params',
'param_name': 'gainref_rotate_num',
'param_type': 'number',
'base_value': 0,
'title': 'Rotate gain ref?',
'desc': 'Rotate gain ref counter-clockwise by 90 degrees this many times'},
{'param_sec': 'mscope_params',
'param_name': 'psize_A',
'param_type': 'number',
'base_value': None,
'title': 'Raw pixel size (A)',
'desc': 'Pixel size of the raw movie data in Angstroms'},
{'param_sec': 'mscope_params',
'param_name': 'accel_kv',
'param_type': 'number',
'base_value': None,
'title': 'Accelerating voltage (kV)',
'desc': ''},
{'param_sec': 'mscope_params',
'param_name': 'cs_mm',
'param_type': 'number',
'base_value': None,
'title': 'Spherical aberration (mm)',
'desc': ''},
{'param_sec': 'mscope_params',
'param_name': 'total_dose_e_per_A2',
'param_type': 'number',
'base_value': None,
'title': 'Total exposure dose (e/A^2)',
'desc': ''},
{'param_sec': 'mscope_params',
'param_name': 'phase_plate',
'param_type': 'boolean',
'base_value': False,
'title': 'Phase plate',
'desc': 'Were the images collected using a phase plate?'},
{'param_sec': 'mscope_params',
'param_name': 'neg_stain',
'param_type': 'boolean',
'base_value': False,
'title': 'Negative stain',
'desc': 'Are the samples negative stain (True) or cryo (False)?'},
{'param_sec': 'mscope_params',
'param_name': 'eer_upsampfactor',
'param_type': 'number',
'base_value': 2,
'title': 'EER upsampling factor',
'desc': 'EER upsampling factor (applies to .eer/.ecc format data only.'},
{'param_sec': 'mscope_params',
'param_name': 'eer_numfractions',
'param_type': 'number',
'base_value': 40,
'title': 'EER number of fractions',
'desc': 'EER number of fractions (applies to .eer/.ecc format data only.'},
{'param_sec': 'motion_settings',
'param_name': 'res_max_align',
'base_value': 5,
'title': 'Maximum alignment resolution (A)',
'param_type': 'number',
'desc': 'Maximum resolution (in A) to consider when aligning frames. Generally, betwen 5A and 3A is best.'},
{'param_sec': 'motion_settings',
'param_name': 'bfactor',
'base_value': 500,
'title': 'B-factor during alignment',
'param_type': 'number',
'desc': 'B-factor that blurs frames before aligning. Generally 500 to 100 is best.'},
{'param_sec': 'motion_settings',
'param_name': 'frame_start',
'base_value': 0,
'title': 'Start frame (included, 0-based)',
'param_type': 'number',
'desc': 'Which frame number, starting at zero, to begin motion correction from. This value controls how many early frames are dropped from the motion corrected result. This value will also be used in local motion correction.'},
{'param_sec': 'motion_settings',
'param_name': 'frame_end',
'base_value': None,
'title': 'End frame (excluded, 0-based) ',
'param_type': 'number',
'desc': 'Which frame number, starting at zero, to not include in motion correction, also excluding all frames after this one. Generally this does not improve results, as later frames are downweighted during dose weighting in local motion correction.'},
{'param_sec': 'motion_settings',
'param_name': 'output_fcrop_factor',
'base_value': 1,
'title': 'Output F-crop factor',
'param_type': 'number',
'desc': 'Output Fourier cropping factor. 1.0 means no cropping, 0.5 means crop to 1/2 the resolution, etc. Only 1, 0.75, 0.5, 0.25 are allowed values'},
{'param_sec': 'motion_settings',
'param_name': 'override_total_exp',
'base_value': None,
'title': 'Override e/A^2',
'param_type': 'number',
'desc': 'Override the dose (in total e/A^2 over the exposure) that was given at import time but can be overridden here.'},
{'param_sec': 'motion_settings',
'param_name': 'variable_dose',
'base_value': False,
'title': 'Allow Variable Dose',
'param_type': 'boolean',
'desc': 'Enable correct processing when frames have variable dose fractionation'},
{'param_sec': 'motion_settings',
'param_name': 'smooth_lambda_cal',
'base_value': 0.5,
'title': 'Calibrated smoothing',
'param_type': 'number',
'desc': 'Calibrated smoothing constant applied to trajectories (None to autotune)'},
{'param_sec': 'motion_settings',
'param_name': 'override_K_Z',
'base_value': None,
'title': 'Override knots Z',
'param_type': 'number',
'desc': 'Override automatically selected spline order for Z dimension (time)'},
{'param_sec': 'motion_settings',
'param_name': 'override_K_Y',
'base_value': None,
'title': 'Override knots Y',
'param_type': 'number',
'desc': 'Override automatically selected spline order for Y dimension (vertical)'},
{'param_sec': 'motion_settings',
'param_name': 'override_K_X',
'base_value': None,
'title': 'Override knots X',
'param_type': 'number',
'desc': 'Override automatically selected spline order for X dimension (horizontal)'},
{'param_sec': 'motion_settings',
'param_name': 'optimize_for_gpu_memory',
'base_value': False,
'title': 'Low-memory mode',
'param_type': 'boolean',
'desc': 'If running out of GPU memory, this option can be used to prioritize memory use at the expense of speed (BETA). The results are unchanged.'},
{'param_sec': 'ctf_settings',
'param_name': 'amp_contrast',
'base_value': 0.1,
'title': 'Amplitude Contrast',
'param_type': 'number',
'desc': 'Amplitude constrast to use. Typically 0.07 or 0.1 for cryo-EM data.'},
{'param_sec': 'ctf_settings',
'param_name': 'res_min_align',
'base_value': 25,
'title': 'Minimum resolution (A)',
'param_type': 'number',
'desc': 'Minimum resolution (in A) to consider when estimating CTF.'},
{'param_sec': 'ctf_settings',
'param_name': 'res_max_align',
'base_value': 4,
'title': 'Maximum resolution (A)',
'param_type': 'number',
'desc': 'Maximum resolution (in A) to consider when estimating CTF.'},
{'param_sec': 'ctf_settings',
'param_name': 'df_search_min',
'base_value': 1000,
'title': 'Minimum search defocus (A)',
'param_type': 'number',
'desc': 'Defocus range for gridsearch.'},
{'param_sec': 'ctf_settings',
'param_name': 'df_search_max',
'base_value': 40000,
'title': 'Maximum search defocus (A)',
'param_type': 'number',
'desc': 'Defocus range for gridsearch.'},
{'param_sec': 'ctf_settings',
'param_name': 'do_phase_shift_search_refine',
'base_value': False,
'title': 'Do phase shift search',
'param_type': 'boolean',
'desc': 'Whether to carry out search and refinement over phase shift.'},
{'param_sec': 'ctf_settings',
'param_name': 'phase_shift_min',
'base_value': 0,
'title': 'Min. search phase-shift (rad)',
'param_type': 'number',
'desc': 'Phase-shift range for gridsearch.'},
{'param_sec': 'ctf_settings',
'param_name': 'phase_shift_max',
'base_value': 3.141592653589793,
'title': 'Max. search phase-shift (rad)',
'param_type': 'number',
'desc': 'Phase-shift range for gridsearch.'},
{'param_sec': 'ctf_settings',
'param_name': 'do_phase_shift_refine_only',
'base_value': False,
'title': 'Do phase refine only',
'param_type': 'boolean',
'desc': 'Whether to carry out refinement over phase shift only'},
{'param_sec': 'ctf_settings',
'param_name': 'override_K_Y',
'base_value': None,
'title': 'Override knots Y',
'param_type': 'number',
'desc': 'Override automatically selected spline order for Y dimension (vertical)'},
{'param_sec': 'ctf_settings',
'param_name': 'override_K_X',
'base_value': None,
'title': 'Override knots X',
'param_type': 'number',
'desc': 'Override automatically selected spline order for X dimension (horizontal)'},
{'param_sec': 'ctf_settings',
'param_name': 'classic_mode',
'base_value': False,
'title': 'Classic mode',
'param_type': 'boolean',
'desc': 'Uses the old Patch CTF algorithm (cryoSPARC v.2.15 and earlier) intead of the new one.'},
{'param_sec': 'particle_picking',
'param_name': 'current_picker',
'base_value': 'blob',
'title': 'Current active picker',
'param_type': 'enum',
'enum_keys': ['blob', 'template', 'deep'],
'desc': 'Which picker type to use on future exposures.'},
{'param_sec': 'blob_pick',
'param_name': 'diameter',
'base_value': None,
'title': 'Minimum particle diameter (A)',
'param_type': 'number',
'desc': 'Min Particle diameter (A)'},
{'param_sec': 'blob_pick',
'param_name': 'diameter_max',
'base_value': None,
'title': 'Maximum particle diameter (A)',
'param_type': 'number',
'desc': 'Max Particle diameter (A)'},
{'param_sec': 'blob_pick',
'param_name': 'use_circle',
'base_value': True,
'title': 'Use circular blob',
'param_type': 'boolean',
'desc': ''},
{'param_sec': 'blob_pick',
'param_name': 'use_ellipse',
'base_value': False,
'title': 'Use elliptical blob',
'param_type': 'boolean',
'desc': ''},
{'param_sec': 'blob_pick',
'param_name': 'use_ring',
'base_value': False,
'title': 'Use ring blob',
'param_type': 'boolean',
'desc': ''},
{'param_sec': 'blob_pick',
'param_name': 'lowpass_res_template',
'base_value': 20,
'title': 'Lowpass filter to apply to templates (A)',
'param_type': 'number',
'desc': 'Lowpass filter to apply to templates, (A)s'},
{'param_sec': 'blob_pick',
'param_name': 'lowpass_res',
'base_value': 20,
'title': 'Lowpass filter to apply (A)',
'param_type': 'number',
'desc': 'Lowpass filter to apply, (A)s'},
{'param_sec': 'blob_pick',
'param_name': 'angular_spacing_deg',
'base_value': 5,
'title': 'Angular sampling (degrees)',
'param_type': 'number',
'desc': 'Angular sampling of templates in degrees. Lower value will mean finer rotations.'},
{'param_sec': 'blob_pick',
'param_name': 'use_ctf',
'base_value': False,
'title': 'Use CTFs to filter the templates',
'param_type': 'boolean',
'desc': 'Whether to use micrograph CTF to filter the templates'},
{'param_sec': 'blob_pick',
'param_name': 'min_distance',
'base_value': 1.0,
'title': 'Min. separation dist (diameters)',
'param_type': 'number',
'desc': 'Minimum distance between particles in units of particle diameter (min diameter for blob picker). The lower this value, the more and closer particles it picks.'},
{'param_sec': 'blob_pick',
'param_name': 'num_process',
'base_value': None,
'title': 'Number of mics to process',
'param_type': 'number',
'desc': 'Number of micrographs to process. None means all.'},
{'param_sec': 'blob_pick',
'param_name': 'num_plot',
'base_value': 10,
'title': 'Number of mics to plot',
'param_type': 'number',
'desc': 'Number of micrographs to plot.'},
{'param_sec': 'blob_pick',
'param_name': 'max_num_hits',
'base_value': 4000,
'title': 'Maximum number of local maxima to consider',
'param_type': 'number',
'desc': 'Maximum number of local maxima (peaks) considered.'},
{'param_sec': 'template_pick',
'param_name': 'diameter',
'base_value': None,
'title': 'Particle diameter (A)',
'param_type': 'number',
'desc': 'Particle diameter (A)'},
{'param_sec': 'template_pick',
'param_name': 'lowpass_res_template',
'base_value': 20,
'title': 'Lowpass filter to apply to templates (A)',
'param_type': 'number',
'desc': 'Lowpass filter to apply to templates, (A)s'},
{'param_sec': 'template_pick',
'param_name': 'lowpass_res',
'base_value': 20,
'title': 'Lowpass filter to apply (A)',
'param_type': 'number',
'desc': 'Lowpass filter to apply, (A)s'},
{'param_sec': 'template_pick',
'param_name': 'angular_spacing_deg',
'base_value': 5,
'title': 'Angular sampling (degrees)',
'param_type': 'number',
'desc': 'Angular sampling of templates in degrees. Lower value will mean finer rotations.'},
{'param_sec': 'template_pick',
'param_name': 'use_ctf',
'base_value': True,
'title': 'Use CTFs to filter the templates',
'param_type': 'boolean',
'desc': 'Whether to use micrograph CTF to filter the templates'},
{'param_sec': 'template_pick',
'param_name': 'min_distance',
'base_value': 0.5,
'title': 'Min. separation dist (diameters)',
'param_type': 'number',
'desc': 'Minimum distance between particles in units of particle diameter. The lower this value, the more and closer particles it picks.'},
{'param_sec': 'template_pick',
'param_name': 'num_process',
'base_value': None,
'title': 'Number of mics to process',
'param_type': 'number',
'desc': 'Number of micrographs to process. None means all.'},
{'param_sec': 'template_pick',
'param_name': 'num_plot',
'base_value': 10,
'title': 'Number of mics to plot',
'param_type': 'number',
'desc': 'Number of micrographs to plot.'},
{'param_sec': 'template_pick',
'param_name': 'max_num_hits',
'base_value': 4000,
'title': 'Maximum number of local maxima to consider',
'param_type': 'number',
'desc': 'Maximum number of local maxima (peaks) considered.'},
{'param_sec': 'template_pick',
'param_name': 'templates_from_job',
'base_value': None,
'title': 'Tempates from job (PX.JXX)',
'param_type': 'string'},
{'param_sec': 'template_pick',
'param_name': 'templates_selected',
'base_value': None,
'title': 'Templates selected (comma sep)',
'param_type': 'string'},
{'param_sec': 'extraction',
'param_name': 'thresh_score_min',
'base_value': None,
'title': 'Score threshold min',
'param_type': 'number',
'desc': 'Minimum picking score threshold'},
{'param_sec': 'extraction',
'param_name': 'thresh_power_min',
'base_value': None,
'title': 'Power threshold min',
'param_type': 'number',
'desc': 'Minimum picking power threshold'},
{'param_sec': 'extraction',
'param_name': 'thresh_power_max',
'base_value': None,
'title': 'Power threshold max',
'param_type': 'number',
'desc': 'Maximum picking power threshold'},
{'param_sec': 'extraction',
'param_name': 'box_size_pix',
'base_value': None,
'title': 'Extraction box size (pix)',
'param_type': 'number',
'desc': 'Size of box to be extracted from micrograph.'},
{'param_sec': 'extraction',
'param_name': 'bin_size_pix',
'base_value': None,
'title': 'Fourier crop to box size (pix)',
'param_type': 'number',
'desc': 'Size of particle boxes after they have been extracted. None means use the same as the extraction box size'}] 