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Sim microscopy

VirtualMicroscope Module Documentation#

This module defines the VirtualMicroscope class and related utility classes and functions for simulating a virtual microscope. The module leverages various components such as cameras, lasers, sample planes, and photophysics to simulate imaging processes.

Table of Contents#

VirtualMicroscope#

The VirtualMicroscope class represents a virtual microscope that integrates various components to simulate imaging processes.

Attributes#

  • camera: Tuple containing a Detector and QuantumEfficiency object.
  • qe: Quantum efficiency of the camera.
  • sample_plane: A SamplePlane object representing the sample being imaged.
  • lasers: Dictionary of LaserProfile objects, keyed by laser names.
  • channels: A Channels object representing the imaging channels.
  • psf: A callable that generates a PSFEngine based on input parameters.
  • _time: Current simulation time in milliseconds.
  • config: A ConfigList object containing configuration parameters.
  • initial_config: Cached initial configuration of the microscope.

Methods#

__init__(self, camera: Tuple[Detector, QuantumEfficiency], sample_plane: SamplePlane, lasers: Dict[str, LaserProfile], channels: Channels, psf: Callable[[float | int, Optional[float | int]], PSFEngine], config: ConfigList, start_time: int = 0)#

Initializes the VirtualMicroscope with the provided components.

_set_laser_position_center_cell(self) -> None#

Centers the laser positions at the center of the sample plane.

_cached_initial_config(self) -> None#

Caches the initial configuration of the microscope.

_set_laser_powers(self, laser_power: Dict[str, float]) -> None#

Sets the power of the lasers. Raises a ValueError if the provided power exceeds the maximum allowed power.

_set_laser_positions(self, laser_positions: Dict[str, Tuple[float, float, float]]) -> None#

Sets the positions of the lasers.

run_sim(self, z_val: float, laser_power:Dict[str, Union[float, Callable[[float], float]], xyoffset: Tuple[float, float], laser_position: Optional[Dict[str, Union[Tuple[float, float, float], Callable[[float], Tuple[float, float, float]]]]] = None, duration_total: Optional[int] = None, exposure_time: Optional[int] = None, interval_time: Optional[int] = None, scanning: Optional[bool] = False) -> Tuple[np.ndarray, MetaData]#

Runs the simulation for the given parameters and returns the resulting image stack and metadata.

reset_to_initial_config(self) -> bool#

Resets the microscope to its initial configuration.

mapSampleCamera#

The mapSampleCamera class maps the location of the sample plane onto the detector grid.

Attributes#

  • sampleplane: A SamplePlane object.
  • camera: A Detector object.
  • xyoffset: Tuple representing the offset in micrometers.
  • frames: Number of frames to process.

Methods#

__post_init__(self)#

Initializes the PhotonFrameContainer with base frames.

get_pixel_indices(self, x: float, y: float) -> Tuple[int, int]#

Converts sample plane coordinates to detector grid indices.

add_psf_frame(self, psf: np.ndarray, mol_pos: Tuple[float, float], frame_num: int) -> None#

Adds a PSF to the specified frame at the given molecular position.

get_frame(self, frame_num: int) -> np.ndarray#

Returns the specified frame.

PhotonFrameContainer#

The PhotonFrameContainer class is a container for simulation frames.

Attributes#

  • frames: List of np.ndarray representing the frames.

Methods#

__iter__(self)#

Allows iteration over the frames.

__len__(self)#

Returns the number of frames.

Utility Functions#

generate_sampling_pattern#

Generates a sampling pattern based on exposure and interval times.

Parameters#
  • exposure_time: Duration of each exposure.
  • interval_time: Duration between exposures.
  • start_time: Beginning of the sampling period.
  • end_time: End of the sampling period.
  • oversample_motion_time: Time resolution for oversampling.
Returns#
  • times: List of sampling times.
  • sample_bool: List indicating frame numbers or intervals.
  • max_frame: Maximum frame number.

timeValidator#

Validates the provided time parameters against the simulation constraints.

Parameters#
  • oexposure_time: Original exposure time.
  • ointerval_time: Original interval time.
  • oversample_motion_time: Time resolution for oversampling.
  • ototal_time: Original total time.
  • current_time: Current simulation time.
  • state_arr: Dictionary containing exposure, interval, and total time.
Returns#
  • duration_total: Validated total duration.
  • exposure_time: Validated exposure time.
  • interval_time: Validated interval time.
Raises#
  • ValueError: If the provided times are invalid.