linumpy.geometry.crop#

Volume cropping and interface-based masking.

Functions#

crop_volume(vol[, xlim, ylim, zlim])

Crops the given volume according to the range given as input.

crop_z0_whole_slice(vol[, dz, nz, voxdim, z0, ...])

Crop whole slice in the z direction.

mask_under_interface(vol, interface[, return_mask])

Create a boolean mask for all voxels at or below the interface depth.

apply_interface_correction(vol, interface)

Apply interface depth correction using linear interpolation.

crop_below_interface(vol_zxy, depth_um, resolution_um)

Crop an OME-Zarr volume to a specified depth below the tissue interface.

Module Contents#

linumpy.geometry.crop.crop_volume(vol, xlim=None, ylim=None, zlim=None)[source]#

Crops the given volume according to the range given as input.

Parameters:

  • vol (ndarray) – Volume to crop

  • xlim ((2,) list) – x range to keep

  • ylim ((2,) list) – y range to keep

  • zlim ((2,) list) – z range to keep

Returns:

Cropped volume

Return type:

ndarray

Notes

  • xlim=[0,-1] means that the whole volume in the x dimension will be returned.

linumpy.geometry.crop.crop_z0_whole_slice(vol, dz=20.0, nz=200.0, voxdim=(1, 1, 1), z0=None, verbose=False, mask=None, return_z0=False)[source]#

Crop whole slice in the z direction.

Parameters:

  • vol (ndarray) – Input volume to crop.

  • dz (float) – Margin in microns under the interface to crop (to remove cutting deformations).

  • nz (float) – Size of the slice to crop in microns.

  • voxdim (tuple of int) – Dimension of each voxel in micron/pixel.

  • z0 (float, optional) – Interface position in microns. If None, it is detected automatically.

  • verbose (bool) – If True, print debug information.

  • mask (ndarray, optional) – Tissue mask. If provided, used to compute the tissue interface.

  • return_z0 (bool) – If True, also return the interface position z0.

Returns:

Cropped array

Return type:

ndarray

linumpy.geometry.crop.mask_under_interface(vol, interface, return_mask=False)[source]#

Create a boolean mask for all voxels at or below the interface depth.

Parameters:
Return type:

numpy.ndarray

linumpy.geometry.crop.apply_interface_correction(vol, interface)[source]#

Apply interface depth correction using linear interpolation.

Parameters:

  • vol (ndarray) – Volume to fix.

  • interface (ndarray) – Tissue interface depth.

Returns:

Fixed volume.

Return type:

ndarray

linumpy.geometry.crop.crop_below_interface(vol_zxy, depth_um, resolution_um, sigma_xy=3.0, sigma_z=2.0, crop_before_interface=False, percentile_clip=None)[source]#

Crop an OME-Zarr volume to a specified depth below the tissue interface.

Detects the water/tissue interface using gradient analysis, then crops the volume to retain only depth_um microns below the interface.

Parameters:

  • vol_zxy (np.ndarray) – Volume with shape (Z, X, Y) as returned by read_omezarr.

  • depth_um (float) – Target depth below interface in microns.

  • resolution_um (float) – Z resolution in microns per voxel.

  • sigma_xy (float) – XY smoothing sigma for interface detection.

  • sigma_z (float) – Z smoothing sigma for interface detection.

  • crop_before_interface (bool) – If True, also crop the volume above the detected interface.

  • percentile_clip (float or None) – If provided, clip values above this percentile before interface detection.

Returns:

  • np.ndarray – Cropped volume (Z’, X, Y).

  • int – Detected interface depth in Z voxels.

Return type:

tuple[numpy.ndarray, int]