acryo.pick package

Module contents

class acryo.pick.DoGPicker(sigma_low: float = 3.5, sigma_high: float = 5.0)

Bases: BasePickerModel

Particle picking based on Difference of Gaussian.

get_params_and_depth(scale: float)

pick_in_chunk(image: ndarray[tuple[int, ...], dtype[float32]], sigma_low: float, sigma_high: float) → tuple[ndarray[tuple[int, ...], dtype[float32]], ndarray[tuple[int, ...], dtype[uint16]], Any]

Pick molecules inside a chunk of image.

class acryo.pick.LoGPicker(sigma: float = 3.5)

Bases: BasePickerModel

Particle picking based on Laplacian of Gaussian.

get_params_and_depth(scale: float)

pick_in_chunk(image: ndarray[tuple[int, ...], dtype[float32]], sigma: float) → tuple[ndarray[tuple[int, ...], dtype[float32]], ndarray[tuple[int, ...], dtype[uint16]], Any]

Pick molecules inside a chunk of image.

class acryo.pick.ZNCCTemplateMatcher(template: ndarray[tuple[int, ...], dtype[float32]] | ImageProvider, rotation: tuple[tuple[float, float], tuple[float, float], tuple[float, float]] | Rotation | None = None, tilt: TiltSeriesModel | None = None, order: int = 1)

Bases: BaseTemplateMatcher

Particle picking based on ZNCC template matching.

Parameters:

• image (da.Array) – The input image.

• scale (float) – The scale of the image.

• min_distance (float) – The minimum distance between the picked particles.

• min_score (float) – The minimum score of the picked particles.

• boundary (str) – The boundary condition for the template matching.

pick_in_chunk(image: ndarray[tuple[int, ...], dtype[float32]], templates: list[ndarray[tuple[int, ...], dtype[float32]]], min_distance: float, min_score: float)

Pick molecules inside a chunk of image.

pick_molecules(image: Array, scale: float = 1.0, *, min_distance: float = 1.0, min_score: float = 0.02, boundary='nearest') → Molecules

Pick molecules from image.