Arbitrary shape

simtissue.arbitrary_shape.checkerboard_mask(shape=[54, 1000, 1100], cube_square_size=100)

Generate checkerboard cell mask

Parameters:

• shape (list[int]) – dimension of the mask [z,y,x]

• cube_square_size – size of the cube in pixel

Returns:

checkerboard mask

simtissue.arbitrary_shape.generate_ellipse(masks: ndarray, cell_id: int, radius_zyx: list = None, rad_min: float = 0.5, rad_max: float = 2)

generate nuclei as ellipse in the chosen cell

Parameters:

• masks (np.ndarray) – cell mask

• cell_id (int) – index of the chosen cell

• radius_zyx – list [Rz, Ry, Rx] of the fix parameter of the elipse leave it None to choose these parameter randomly between rad_min and rad_max

• rad_min (float) – Min value of the radius if radius_zyx is None

• rad_max – Max value of the radius if radius_zyx is None

Returns:

ellipse mask , ellipse parameter

simtissue.arbitrary_shape.add_sphere_nuclei(mask_cyto: ndarray, cube_square_size: int = 100, nuclei_radius: int = 25, list_nuclei: list = [])

add nuclei as sphere in the chosen cell

Parameters:

• mask_cyto (np.ndarray) – cell mask

• cube_square_size (int) – size of the cube in pixel

• nuclei_radius (float) – radius of the nuclei in pixel in pourcentage of the cube_square_size

• list_nuclei (list) – list of nuclei to add

Returns:

mask of the nuclei

simtissue.arbitrary_shape.remove_nuclei(mask_nuclei: ndarray, percent_to_remove: float = 0.5, list_nuc_to_keep: list = None)

remove nuclei from the existing nuclei mask to generate cell without nuclei like in smFISH experiment

Parameters:

• mask_nuclei (np.ndarray) – nuclei mask

• percent_to_remove (float) – percent of nuclei to remove

• list_nuc_to_keep (list) – list of nuclei to keep

Returns:

mask of the nuclei without some nuclei

simtissue.arbitrary_shape.elbow_grid_cube()

Function to generate grid of elbow shape. the size of the cell mask is hard coded to 1800x1600 and the size square cell is 100 pixel, the size of nuclei is 25 pixel

Returns:

mask_cyto, mask_nuclei