smlmlp.image_smlm3d module

smlmlp.image_smlm3d(col, /, xx, yy, crlb=None, weight=1.0, x_shape=None, y_shape=None, shape=None, *, image_sigma=None, pixel_sr_nm=15.0, z_pixel=None, col_pixel=None, z_bins=None, z_min=None, z_max=None, x0=None, y0=None, crop_sigma=4.0, max_radius_pixels=0, cuda=False, parallel=False)[source]

Render localizations into a 3D SMLM volume using col as z coordinate.

Each localization contributes a 2D integrated Gaussian in the z plane selected from col. This keeps the expensive Gaussian integration in xy while avoiding artificial blur along arbitrary metadata dimensions.

Parameters:

  • col (array-like) – Values defining the third dimension.

  • xx (array-like) – Localization coordinates in nm.

  • yy (array-like) – Localization coordinates in nm.

  • crlb (float or array-like, optional) – Gaussian sigma in nm. image_sigma takes precedence over crlb.

  • image_sigma (float or array-like, optional) – Gaussian sigma in nm. image_sigma takes precedence over crlb.

  • weight (float or array-like, optional) – Integrated weight of each localization.

  • z_pixel (float, optional) – Bin size for the third dimension. Defaults to the render pixel size.

  • col_pixel (float, optional) – Bin size for the third dimension. Defaults to the render pixel size.

  • z_bins (int or array-like, optional) – Explicit number of z bins or bin edges. If provided, overrides z_pixel for z indexing.

  • z_min (float, optional) – z range limits. Defaults to finite extrema of col.

  • z_max (float, optional) – z range limits. Defaults to finite extrema of col.

Returns:

  • volume (ndarray) – float32 array with shape (z, y, x).

  • info (dict) – Rendering and z-bin metadata.