session_params

session_params#

Classes:

`LiveAbinitParams`	Parameters for Live Ab-initio Reconstruction
`LiveClass2DParams`	Parameters for Streaming 2D Classification
`LivePreprocessingParams`	Live session pre-processing parameter definitions.
`LiveRefineParams`	Parameters for Streaming Homogeneous Refinement

class LiveAbinitParams#

Parameters for Live Ab-initio Reconstruction

Attributes:

`abinit_K`	Number of Ab-Initio classes
`abinit_num_particles`	Number of particles to use
`abinit_symmetry`	Symmetry

abinit_K: int#: Number of Ab-Initio classes

abinit_num_particles: int | None#: Number of particles to use

abinit_symmetry: str#: Symmetry

class LiveClass2DParams#

Parameters for Streaming 2D Classification

Attributes:

`class2D_K`	Number of classes
`class2D_max_res`	Maximum resolution (Å)
`class2D_window_inner_A`	Circular mask diameter (Å)
`compute_use_ssd`	Whether to cache particle images on SSD
`psize_mic`	Pixel size (Å) of the input micrographs :meta private:

class2D_K: int#: Number of classes

class2D_max_res: int#: Maximum resolution (Å)

class2D_window_inner_A: float | None#: Circular mask diameter (Å)

compute_use_ssd: bool#: Whether to cache particle images on SSD

psize_mic: float | None#: Pixel size (Å) of the input micrographs :meta private:

class LivePreprocessingParams#

Live session pre-processing parameter definitions.

Attributes:

`accel_kv`
`amp_contrast`	Amplitude constrast to use.
`bfactor`	B-factor that blurs frames before aligning.
`bin_size_pix`	Size of particle boxes after they have been extracted.
`blob_angular_spacing_deg`	Angular sampling of templates in degrees.
`blob_diameter_max`	Max Particle diameter (Å)
`blob_diameter_min`	Min Particle diameter (Å)
`blob_lowpass_res`	Lowpass filter to apply, (Å)s
`blob_lowpass_res_template`	Lowpass filter to apply to templates, (Å)s
`blob_max_num_hits`	Maximum number of local maxima (peaks) considered.
`blob_min_distance`	Minimum distance between particles in units of particle diameter (min diameter for blob picker).
`blob_num_plot`	Number of micrographs to plot.
`blob_num_process`	Number of micrographs to process.
`blob_use_ctf`	Whether to use micrograph CTF to filter the templates
`box_size_pix`	Size of box to be extracted from micrograph.
`classic_mode`	Uses the old Patch CTF algorithm (cryoSPARC v.2.15 and earlier) intead of the new one.
`cs_mm`
`ctf_override_K_X`	Override automatically selected spline order for X dimension (horizontal)
`ctf_override_K_Y`	Override automatically selected spline order for Y dimension (vertical)
`ctf_res_max_align`	Maximum resolution (in Å) to consider when estimating CTF.
`ctf_res_min_align`	Minimum resolution (in Å) to consider when estimating CTF.
`current_picker`	Which picker type to use on future exposures.
`df_search_max`	Defocus range for gridsearch.
`df_search_min`	Defocus range for gridsearch.
`do_phase_shift_refine_only`	Whether to carry out refinement over phase shift only
`do_phase_shift_search_refine`	Whether to carry out search and refinement over phase shift.
`do_plotting`	Enable plotting in the RTP Worker for every 20 movies processed.
`eer_numfractions`	EER number of fractions (applies to .eer/.ecc format data only.
`eer_upsampfactor`	EER upsampling factor (applies to .eer/.ecc format data only.
`extract_f16`	Reduces the output precision from 32 bits to 16 bits, saving hard drive space.
`frame_end`	Which frame number, starting at zero, to not include in motion correction, also excluding all frames after this one.
`frame_start`	Which frame number, starting at zero, to begin motion correction from.
`gainref_flip_x`	Flip gain ref left-to-right (in X axis)
`gainref_flip_y`	Flip gain ref top-to-bottom (in Y axis)
`gainref_rotate_num`	Rotate gain ref counter-clockwise by 90 degrees this many times
`motion_override_K_X`	Override automatically selected spline order for X dimension (horizontal)
`motion_override_K_Y`	Override automatically selected spline order for Y dimension (vertical)
`motion_override_K_Z`	Override automatically selected spline order for Z dimension (time)
`motion_res_max_align`	Maximum resolution (in Å) to consider when aligning frames.
`neg_stain`	Are the samples negative stain (True) or cryo (False)?
`optimize_for_gpu_memory`	If running out of GPU memory, this option can be used to prioritize memory use at the expense of speed (BETA).
`output_f16`	Reduces the output precision from 32 bits to 16 bits, saving hard drive space.
`output_fcrop_factor`	Output Fourier cropping factor.
`override_total_exp`	Override the dose (in total e/Å^2 over the exposure) that was given at import time but can be overridden here.
`phase_plate`	Were the images collected using a phase plate?
`phase_shift_max`	Phase-shift range for gridsearch.
`phase_shift_min`	Phase-shift range for gridsearch.
`psize_A`	Pixel size of the raw movie data in Angstroms
`smooth_lambda_cal`	Calibrated smoothing constant applied to trajectories (None to autotune)
`template_angular_spacing_deg`	Angular sampling of templates in degrees.
`template_diameter`	Particle diameter (Å)
`template_lowpass_res`	Lowpass filter to apply, (Å)s
`template_lowpass_res_template`	Lowpass filter to apply to templates, (Å)s
`template_max_num_hits`	Maximum number of local maxima (peaks) considered.
`template_min_distance`	Minimum distance between particles in units of particle diameter.
`template_num_plot`	Number of micrographs to plot.
`template_num_process`	Number of micrographs to process.
`template_use_ctf`	Whether to use micrograph CTF to filter the templates
`templates_from_job`
`templates_selected`
`thresh_power_max`	Maximum picking power threshold
`thresh_power_min`	Minimum picking power threshold
`thresh_score_min`	Minimum picking score threshold
`total_dose_e_per_A2`
`use_circle`
`use_ellipse`
`use_ring`
`variable_dose`	Enable correct processing when frames have variable dose fractionation

accel_kv: float#

amp_contrast: float#: Amplitude constrast to use. Typically 0.07 or 0.1 for cryo-EM data.

bfactor: float#: B-factor that blurs frames before aligning. Generally 500 to 100 is best.

bin_size_pix: int | None#: Size of particle boxes after they have been extracted. None means use the same as the extraction box size

blob_angular_spacing_deg: float#: Angular sampling of templates in degrees. Lower value will mean finer rotations.

blob_diameter_max: float#: Max Particle diameter (Å)

blob_diameter_min: float#: Min Particle diameter (Å)

blob_lowpass_res: float#: Lowpass filter to apply, (Å)s

blob_lowpass_res_template: float#: Lowpass filter to apply to templates, (Å)s

blob_max_num_hits: int#: Maximum number of local maxima (peaks) considered.

blob_min_distance: float#: 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.

blob_num_plot: int#: Number of micrographs to plot.

blob_num_process: int | None#: Number of micrographs to process. None means all.

blob_use_ctf: bool#: Whether to use micrograph CTF to filter the templates

box_size_pix: int#: Size of box to be extracted from micrograph.

classic_mode: bool#: Uses the old Patch CTF algorithm (cryoSPARC v.2.15 and earlier) intead of the new one.

cs_mm: float#

ctf_override_K_X: int | None#: Override automatically selected spline order for X dimension (horizontal)

ctf_override_K_Y: int | None#: Override automatically selected spline order for Y dimension (vertical)

ctf_res_max_align: float#: Maximum resolution (in Å) to consider when estimating CTF.

ctf_res_min_align: float#: Minimum resolution (in Å) to consider when estimating CTF.

current_picker: Literal['blob', 'template', 'deep']#: Which picker type to use on future exposures.

df_search_max: float#: Defocus range for gridsearch.

df_search_min: float#: Defocus range for gridsearch.

do_phase_shift_refine_only: bool#: Whether to carry out refinement over phase shift only

do_phase_shift_search_refine: bool#: Whether to carry out search and refinement over phase shift.

do_plotting: bool#: Enable plotting in the RTP Worker for every 20 movies processed.

eer_numfractions: int#: EER number of fractions (applies to .eer/.ecc format data only.

eer_upsampfactor: int#: EER upsampling factor (applies to .eer/.ecc format data only.

extract_f16: bool#: Reduces the output precision from 32 bits to 16 bits, saving hard drive space.

frame_end: int | None#: 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.

frame_start: int#: 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.

gainref_flip_x: bool#: Flip gain ref left-to-right (in X axis)

gainref_flip_y: bool#: Flip gain ref top-to-bottom (in Y axis)

gainref_rotate_num: int#: Rotate gain ref counter-clockwise by 90 degrees this many times

motion_override_K_X: int | None#: Override automatically selected spline order for X dimension (horizontal)

motion_override_K_Y: int | None#: Override automatically selected spline order for Y dimension (vertical)

motion_override_K_Z: int | None#: Override automatically selected spline order for Z dimension (time)

motion_res_max_align: float#: Maximum resolution (in Å) to consider when aligning frames. Generally, betwen 5Å and 3Å is best.

neg_stain: bool#: Are the samples negative stain (True) or cryo (False)?

optimize_for_gpu_memory: bool#: 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.

output_f16: bool#: Reduces the output precision from 32 bits to 16 bits, saving hard drive space.

output_fcrop_factor: float#: 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

override_total_exp: float | None#: Override the dose (in total e/Å^2 over the exposure) that was given at import time but can be overridden here.

phase_plate: bool#: Were the images collected using a phase plate?

phase_shift_max: float#: Phase-shift range for gridsearch.

phase_shift_min: float#: Phase-shift range for gridsearch.

psize_A: float#: Pixel size of the raw movie data in Angstroms

smooth_lambda_cal: float#: Calibrated smoothing constant applied to trajectories (None to autotune)

template_angular_spacing_deg: float#: Angular sampling of templates in degrees. Lower value will mean finer rotations.

template_diameter: float | None#: Particle diameter (Å)

template_lowpass_res: float#: Lowpass filter to apply, (Å)s

template_lowpass_res_template: float#: Lowpass filter to apply to templates, (Å)s

template_max_num_hits: int#: Maximum number of local maxima (peaks) considered.

template_min_distance: float#: Minimum distance between particles in units of particle diameter. The lower this value, the more and closer particles it picks.

template_num_plot: int#: Number of micrographs to plot.

template_num_process: int | None#: Number of micrographs to process. None means all.

template_use_ctf: bool#: Whether to use micrograph CTF to filter the templates

templates_from_job: str | None#

templates_selected: str | None#

thresh_power_max: float | None#: Maximum picking power threshold

thresh_power_min: float | None#: Minimum picking power threshold

thresh_score_min: float#: Minimum picking score threshold

total_dose_e_per_A2: float#

use_circle: bool#

use_ellipse: bool#

use_ring: bool#

variable_dose: bool#: Enable correct processing when frames have variable dose fractionation

class LiveRefineParams#

Parameters for Streaming Homogeneous Refinement

Attributes:

`psize_mic`	Pixel size (Å) of the input micrographs :meta private:
`refine_symmetry`	Symmetry

psize_mic: float | None#: Pixel size (Å) of the input micrographs :meta private:

refine_symmetry: str#: Symmetry

session_params

Contents

session_params#