CopickTiltSeriesMetadata

Bases: BaseModel

Metadata of a tilt series: the image geometry, the microscope and, per image, acquisition and CTF data.

Stored CETS-shaped in the copick attributes of the tilt series' Zarr group (see copick.util.cets).

Attributes:

• pixel_size (float) –

  Pixel size of the full-size images in Angstrom, rounded to the third decimal.

• width (int) –

  Width of the full-size images in pixels.

• height (int) –

  Height of the full-size images in pixels.

• images (List[CopickTiltImage]) –

  Per-image data, one entry per section ordered by section, or empty if unknown.

• tilt_axis_angle (Optional[float]) –

  Nominal in-plane angle of the tilt axis in degrees.

• voltage (Optional[float]) –

  Acceleration voltage in kV.

• spherical_aberration (Optional[float]) –

  Spherical aberration in mm.

• amplitude_contrast (Optional[float]) –

  Amplitude contrast as a fraction.

• amplitude_contrast_source (Optional[Literal['source', 'user', 'default']]) –

  Where the amplitude contrast came from: the data source, the user, or a default.

• handedness (Optional[Literal['right_handed', 'left_handed']]) –

  Handedness of the acquisition geometry, if known.

• microscope_model (Optional[str]) –

  Microscope model.

• detector_model (Optional[str]) –

  Detector model.

• is_aligned (bool) –

  Whether the stored images were already aligned (transformed), so per-image alignments do not apply.

• ctf_corrected (bool) –

  Whether the stored images were CTF-corrected.

• native (Dict[str, Any]) –

  Source-specific values without a place in this model, kept for reference.

• provenance (Dict[str, Any]) –

  Where the metadata came from (program, files, portal identifiers).

pixel_size: float

width: int

height: int

images: List[CopickTiltImage] = Field(default_factory=list)

tilt_axis_angle: Optional[float] = None

voltage: Optional[float] = None

spherical_aberration: Optional[float] = None

amplitude_contrast: Optional[float] = None

amplitude_contrast_source: Optional[Literal['source', 'user', 'default']] = None

handedness: Optional[Literal['right_handed', 'left_handed']] = None

microscope_model: Optional[str] = None

detector_model: Optional[str] = None

is_aligned: bool = False

ctf_corrected: bool = False

native: Dict[str, Any] = Field(default_factory=dict)

provenance: Dict[str, Any] = Field(default_factory=dict)

n_sections: int

nominal_tilt_angles: List[Optional[float]]

ctf_status: Literal['absent', 'suspicious', 'partial', 'fitted']

ctf_flags: Dict[str, bool]