Parameter Reference
Complete reference for all parameters accepted by image_vsample and run_parameter_sweep.
Structure Parameters
| Parameter |
Description |
Notes |
| structure |
4-letter PDB ID code, or path to a local structure file |
Any PDB/CIF format file |
| structure_is_path |
Treat structure as a local file path rather than a PDB ID (bool, default False) |
— |
| structure_axis_euler |
Euler angles [α, β, γ] (degrees) to rotate the structure's principal axis before positioning |
Default [0, 0, 0] |
| structure_global_normal_orientation |
Assign a fixed global normal direction for all structure epitopes (list or None) |
— |
| structure_format |
File format of the structure ("CIF" or "PDB"). Inferred from file extension when structure_is_path is True |
Default "CIF" |
Probe Parameters
| Parameter |
Description |
| probe_template |
Name of a pre-set probe configuration file (filename) |
| probe_name |
Optional. Alternative name to identify this probe |
| labelling_efficiency |
Probability that the probe binds a given epitope (float, default 1.0) |
| probe_target_type |
Type of target: "Sequence", "Residue", or "Primary" |
| probe_target_value |
Specific value for the target type (e.g., amino acid sequence, residue info) |
| probe_target_option |
Additional option for the probe target; used for secondary epitopes |
| probe_distance_to_epitope |
Minimum distance from probe to epitope (float) |
| probe_model |
4-letter PDB ID for the atomic model of the probe itself |
| probe_fluorophore |
Fluorophore name for emitters (e.g., "AF647") |
| probe_paratope |
If probe_model is set, the residue anchor point of the probe |
| probe_conjugation_target_info |
If probe_model is set, dictionary specifying emitter conjugation sites |
| probe_DoL |
Degree of labelling — efficiency of fluorophore conjugation (float) |
| probe_secondary_epitope |
Amino acid sequence defining the epitope on a primary antibody model |
| probe_wobble_theta |
Enable probe angular wobble (float or None) |
| probe_steric_hindrance |
Minimum distance between adjacent epitopes (float) |
| peptide_motif |
Dictionary specifying motif extraction for probe target sequence |
| as_primary |
Treat the probe as a primary linker (bool) |
Structural Integrity Parameters
| Parameter |
Description |
| structural_integrity |
Fraction of the particle rendered inaccessible to probes (float, 0–1) |
| structural_integrity_small_cluster |
Maximum distance between epitopes for the first (small) inaccessible cluster grouping (Å) |
| structural_integrity_large_cluster |
Minimum distance between epitopes for the second (large) inaccessible cluster grouping (Å) |
Virtual Sample Parameters
| Parameter |
Description |
| virtual_sample_template |
Name of the configuration file for a virtual sample template |
| sample_dimensions |
X, Y, Z field dimensions in nanometers (list of float) |
| sample_inital_orientation |
Initial orientation applied to all labelled structures in the virtual sample (list or None) |
| number_of_particles |
Number of independent particle copies distributed in the field (int) |
| particle_positions |
Explicit list of relative particle positions (list of arrays) |
| random_orientations |
Randomly assign orientations to each particle (bool, default False) |
| orientation_per_particle |
Explicit list of orientations, one per particle |
| xy_orientations |
List of orientation directions on the XY plane to sample from |
| xz_orientations |
List of orientation directions on the XZ plane to sample from |
| yz_orientations |
List of orientation directions on the YZ plane to sample from |
| axial_offset |
List of Z offsets from the focus plane to sample from |
| random_placing |
Place particles at random positions (bool, default False) |
| random_rotations |
Apply random 3-D rotations to particles (bool, default False) |
| rotation_per_particle |
Explicit list of rotations, one per particle |
| rotation_angles |
List of rotation angles to sample from |
| expansion_factor |
Scale factor applied to the structure coordinates (float, default 1) |
| minimal_distance |
Minimum allowed distance between particles (float) |
| clear_probes |
Clear any probes already added to the experiment before adding new ones (bool, default False) |
| clear_experiment |
Fully reset the experiment object after the simulation (bool, default False) |
Modalities Parameters
| Parameter |
Description |
| pixelsize_nm |
Image pixel size in nanometers (float or int) |
| lateral_resolution_nm |
Lateral (XY) resolution in nanometers (float or int) |
| axial_resolution_nm |
Axial (Z) resolution in nanometers (float or int) |
| psf_voxel_nm |
Voxel size used to render the PSF in nanometers (float or int, default 10) |
| depth_of_field_nm |
Depth of field in nanometers (float or int) |
Multi-Probe Parameters
| Parameter |
Description |
| primary_probe |
Probe template name for the primary label in indirect labelling |
| secondary_probe |
Probe template name for the secondary label in indirect labelling |
| probe_list |
List of probe configuration dictionaries for adding multiple probes in a single call |
| as_primary |
Treat this probe as a primary linker target for a secondary probe (bool) |
Reproducibility
| Parameter |
Description |
| random_seed |
Integer seed passed to numpy.random.seed before any stochastic step (int or None) |
Acquisition Parameters
| Parameter |
Description |
| exp_time |
Exposure time in seconds (float) |
| noise |
Include photon and detector noise in the simulation (bool) |
| nframes |
Number of frames to simulate (int) |