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cryotypes

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cryotypes defines a set of super-simple, extensible data structures for the fundamental types of cryoEM data and their relevant metadata:

  • PoseSet: a set of particle poses, compatible with 2D and 3D data
  • ProjectionModel: a set of parameters for a projection model (tilt-series alignments)
  • Tomogram: a 3D image
  • Micrograph: a 2D image

Each cryotype defines an experiment_id attribute which is intended as a unique identifier for individual experiments. This can be used, for example, to match particles to the correct tilt series and tomogram.

Image

An Image is a dataclass holding a simple data array and some metadata.

Image fields

Field Semantics
data image data (ZYX ordering)
experiment_id identifier for micrograph/tilt-series
pixel_spacing isotropic pixel/voxel spacing
source the source file of this data
stack whether the data represent a stack of 2D images

PoseSet

A PoseSet is a dataclass with a few fields describing positions, orientations and so on for a set of particles. It can be used for both 2D and 3D particle poses.

PoseSet fields

Field Semantics
position particle positions (x, y, z) in pixels
shift particle shifts (x, y, z) in pixels
orientation particle orientation
experiment_id identifier for micrograph/tilt-series
pixel_spacing isotropic pixel/voxel spacing for particle positions
source the source file of this data

Positions

Particle positions are coordinates in 2D or 3D images (for 2D, z is simply set to 0). The center of the first pixel is taken to be the origin (0, 0, 0) and the units of particle positions are pixels.

Shifts

Particle shifts are in image pixels and are additive to positions, such that POSITION + SHIFT is the position of the particle in the tomogram.

Orientations

Particle orientations are stored as scipy.spatial.transform.Rotation objects. These transformations should rotate the basis vectors (ordered xyz) of a reference such that they are correctly oriented in a tomogram.

Note: this yields rotated basis vectored ordered xyz whilst dimensions in an image are normally zyx!

ProjectionModel

A ProjectionModel is a pandas DataFrame with specific column headings for the parameters of a projection model. Together, this information constitues a 'tilt-series alignment'.

Heading Python name Semantics
rotation_x ROTATION_X specimen rotation around x-axis
rotation_y ROTATION_Y specimen rotation around y-axis
rotation_z ROTATION_Z specimen rotation around z-axis
dx SHIFT_X specimen shift in x-dimension of the camera plane
dy SHIFT_Y particle shift in y-dimension of the camera plane
experiment_id EXPERIMENT_ID identifier for micrograph/tilt-series
pixel_spacing PIXEL_SPACING isotropic pixel/voxel spacing for shifts
source SOURCE reference to the file from which data came

In the microsope reference frame, the z-axis is the beam direction. Extrinsic rotation of the tomogram around the x-axis, the y-axis, then the z-axis by rotation_x, rotation_y, rotation_z followed by projection along the z-axis (beam direction) then shifting the 2D image in the camera plane by dx and dy produces the experimental projection image.

A utility function is also provided for generating projection matrices from these data. These projection matrices can be used to calculate a 2D position in a tilt-image from a 3D position in the tomogram.

from cryotypes.projectionmodel import projection_model_to_projection_matrices

projection_matrices = projection_model_to_projection_matrices(
    df=projection_model,  # ProjectionModel dataframe
    tilt_image_center=(1919, 1355),  # tilt-image rotation center (xy)
    tomogram_dimensions=(3838, 3710, 2000)  # dimensions of tomogram (xyz)
)

Note: these projection matrices are only valid for positions in a tomogram of the dimensions provided in this function and must be recalculated for different tomogram dimensions.

Tomogram

A Tomogram is an object that follows a specific python Protocol for tomogram data. The protocol specifies the following attributes:

  • data: an array-like 3D image (numpy, dask, ...)
  • experiment_id: experimental identifier
  • pixel_spacing: isotropic pixel/voxel spacing