Skip to content

Budding Yeast Cell

Budding Yeast Cell Reference#

BuddingCell dataclass #

Bases: BaseCell

Represents a budding yeast cell composed of two connected ovoids (mother and bud). The cells are connected at a "neck" region, with the bud growing from the mother cell.

Attributes:

Name Type Description
center ndarray

The (x, y, z) coordinates of the mother cell's center in XYZ plane
mother_radius_x float

Mother cell radius along X axis
mother_radius_y float

Mother cell radius along Y axis
mother_radius_z float

Mother cell radius along Z axis
bud_radius_x float

Bud radius along X axis
bud_radius_y float

Bud radius along Y axis
bud_radius_z float

Bud radius along Z axis
bud_angle float

Angle in radians from x-axis where bud emerges
bud_distance float

Distance between mother and bud centers
neck_radius float

Radius of the connecting neck region
Source code in SMS_BP/cells/budding_yeast_cell.py 
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
@dataclass
class BuddingCell(BaseCell):
    """
    Represents a budding yeast cell composed of two connected ovoids (mother and bud).
    The cells are connected at a "neck" region, with the bud growing from the mother cell.

    Attributes:
        center (np.ndarray): The (x, y, z) coordinates of the mother cell's center in XYZ plane
        mother_radius_x (float): Mother cell radius along X axis
        mother_radius_y (float): Mother cell radius along Y axis
        mother_radius_z (float): Mother cell radius along Z axis
        bud_radius_x (float): Bud radius along X axis
        bud_radius_y (float): Bud radius along Y axis
        bud_radius_z (float): Bud radius along Z axis
        bud_angle (float): Angle in radians from x-axis where bud emerges
        bud_distance (float): Distance between mother and bud centers
        neck_radius (float): Radius of the connecting neck region
    """

    center: np.ndarray | List[float] | Tuple
    mother_radius_x: float
    mother_radius_y: float
    mother_radius_z: float
    bud_radius_x: float
    bud_radius_y: float
    bud_radius_z: float
    bud_angle: float
    bud_distance: float
    neck_radius: float

    def contains_point_fallback(
        self, x: float, y: float, z: float, tolerance: float = 1e-3
    ) -> bool:
        """
        Determines if a given point is inside the BuddingCell.
        A point is inside if it's within the mother cell, the bud, or the neck region.

        Args:
            point (np.ndarray | List[float] | Tuple): The (x, y, z) coordinates of the point to check

        Returns:
            bool: True if the point is inside the cell, False otherwise
        """
        # Ensure point is a numpy array for vector operations
        point = np.array([x, y, z])
        mother_center = np.array(self.center)

        # Calculate bud center based on angle and distance
        bud_x = mother_center[0] + self.bud_distance * np.cos(self.bud_angle)
        bud_y = mother_center[1] + self.bud_distance * np.sin(self.bud_angle)
        bud_center = np.array([bud_x, bud_y, mother_center[2]])

        # Check if point is inside the mother cell (scaled ellipsoid)
        x, y, z = point - mother_center
        mother_distance_squared = (
            (x / self.mother_radius_x) ** 2
            + (y / self.mother_radius_y) ** 2
            + (z / self.mother_radius_z) ** 2
        )
        if mother_distance_squared <= 1:
            return True

        # Check if point is inside the bud (scaled ellipsoid)
        x, y, z = point - bud_center
        bud_distance_squared = (
            (x / self.bud_radius_x) ** 2
            + (y / self.bud_radius_y) ** 2
            + (z / self.bud_radius_z) ** 2
        )
        if bud_distance_squared <= 1:
            return True

        # Check if point is inside the neck region
        # First, project the point onto the line between mother and bud centers
        mother_to_bud_vec = bud_center - mother_center
        mother_to_bud_length = np.linalg.norm(mother_to_bud_vec)
        mother_to_bud_unit = mother_to_bud_vec / mother_to_bud_length

        mother_to_point_vec = point - mother_center
        projection_length = np.dot(mother_to_point_vec, mother_to_bud_unit)

        # Calculate minimum distance from point to the center line
        if 0 <= projection_length <= mother_to_bud_length:
            projection_point = mother_center + projection_length * mother_to_bud_unit
            distance_to_line = np.linalg.norm(point - projection_point)

            # The neck is modeled as a truncated cone
            # Interpolate the radius at this point along the neck
            if projection_length <= self.mother_radius_x:
                # Within mother cell radius from the center
                local_radius = self.neck_radius
            elif projection_length >= mother_to_bud_length - self.bud_radius_x:
                # Within bud cell radius from the bud center
                local_radius = self.neck_radius
            else:
                local_radius = self.neck_radius

            return distance_to_line <= local_radius

        return False

contains_point_fallback(x, y, z, tolerance=0.001) #

Determines if a given point is inside the BuddingCell. A point is inside if it's within the mother cell, the bud, or the neck region.

Parameters:

Name Type Description Default
point ndarray | List[float] | Tuple

The (x, y, z) coordinates of the point to check

 required

Returns:

Name Type Description
bool bool

True if the point is inside the cell, False otherwise
Source code in SMS_BP/cells/budding_yeast_cell.py 
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
def contains_point_fallback(
    self, x: float, y: float, z: float, tolerance: float = 1e-3
) -> bool:
    """
    Determines if a given point is inside the BuddingCell.
    A point is inside if it's within the mother cell, the bud, or the neck region.

    Args:
        point (np.ndarray | List[float] | Tuple): The (x, y, z) coordinates of the point to check

    Returns:
        bool: True if the point is inside the cell, False otherwise
    """
    # Ensure point is a numpy array for vector operations
    point = np.array([x, y, z])
    mother_center = np.array(self.center)

    # Calculate bud center based on angle and distance
    bud_x = mother_center[0] + self.bud_distance * np.cos(self.bud_angle)
    bud_y = mother_center[1] + self.bud_distance * np.sin(self.bud_angle)
    bud_center = np.array([bud_x, bud_y, mother_center[2]])

    # Check if point is inside the mother cell (scaled ellipsoid)
    x, y, z = point - mother_center
    mother_distance_squared = (
        (x / self.mother_radius_x) ** 2
        + (y / self.mother_radius_y) ** 2
        + (z / self.mother_radius_z) ** 2
    )
    if mother_distance_squared <= 1:
        return True

    # Check if point is inside the bud (scaled ellipsoid)
    x, y, z = point - bud_center
    bud_distance_squared = (
        (x / self.bud_radius_x) ** 2
        + (y / self.bud_radius_y) ** 2
        + (z / self.bud_radius_z) ** 2
    )
    if bud_distance_squared <= 1:
        return True

    # Check if point is inside the neck region
    # First, project the point onto the line between mother and bud centers
    mother_to_bud_vec = bud_center - mother_center
    mother_to_bud_length = np.linalg.norm(mother_to_bud_vec)
    mother_to_bud_unit = mother_to_bud_vec / mother_to_bud_length

    mother_to_point_vec = point - mother_center
    projection_length = np.dot(mother_to_point_vec, mother_to_bud_unit)

    # Calculate minimum distance from point to the center line
    if 0 <= projection_length <= mother_to_bud_length:
        projection_point = mother_center + projection_length * mother_to_bud_unit
        distance_to_line = np.linalg.norm(point - projection_point)

        # The neck is modeled as a truncated cone
        # Interpolate the radius at this point along the neck
        if projection_length <= self.mother_radius_x:
            # Within mother cell radius from the center
            local_radius = self.neck_radius
        elif projection_length >= mother_to_bud_length - self.bud_radius_x:
            # Within bud cell radius from the bud center
            local_radius = self.neck_radius
        else:
            local_radius = self.neck_radius

        return distance_to_line <= local_radius

    return False

make_BuddingCell(center, mother_radius_x, mother_radius_y, mother_radius_z, bud_radius_x, bud_radius_y, bud_radius_z, bud_angle, bud_distance, neck_radius) #

Create a budding yeast cell using PyVista meshes.

Parameters:

Name Type Description Default
center ndarray | List[float] | Tuple

Center point of the mother cell

 required
mother_radius_x/y/z

Radii of the mother cell along each axis

 required
bud_radius_x/y/z

Radii of the bud cell along each axis

 required
bud_angle float

Angle in radians from x-axis where bud emerges

 required
bud_distance float

Distance between mother and bud centers

 required
neck_radius float

Radius of the connecting neck region

 required

Returns:

Name Type Description
BuddingCell BuddingCell

Instance with PyVista mesh
Source code in SMS_BP/cells/budding_yeast_cell.py 
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
def make_BuddingCell(
    center: np.ndarray | List[float] | Tuple,
    mother_radius_x: float,
    mother_radius_y: float,
    mother_radius_z: float,
    bud_radius_x: float,
    bud_radius_y: float,
    bud_radius_z: float,
    bud_angle: float,
    bud_distance: float,
    neck_radius: float,
) -> BuddingCell:
    """
    Create a budding yeast cell using PyVista meshes.

    Args:
        center: Center point of the mother cell
        mother_radius_x/y/z: Radii of the mother cell along each axis
        bud_radius_x/y/z: Radii of the bud cell along each axis
        bud_angle: Angle in radians from x-axis where bud emerges
        bud_distance: Distance between mother and bud centers
        neck_radius: Radius of the connecting neck region

    Returns:
        BuddingCell: Instance with PyVista mesh
    """
    # Validate inputs
    center = np.array(center)
    if center.shape != (3,):
        raise ValueError("Center must be a 3D point")

    # Calculate bud center
    bud_center = np.array(
        [
            center[0] + bud_distance * np.cos(bud_angle),
            center[1] + bud_distance * np.sin(bud_angle),
            center[2],
        ]
    )

    # Create mother cell ellipsoid
    mother = pv.ParametricEllipsoid(
        xradius=mother_radius_x,
        yradius=mother_radius_y,
        zradius=mother_radius_z,
        center=center,
    )

    # Create bud cell ellipsoid
    bud = pv.ParametricEllipsoid(
        xradius=bud_radius_x,
        yradius=bud_radius_y,
        zradius=bud_radius_z,
        center=bud_center,
    )

    # Create neck region (cylinder)
    # Calculate direction vector from mother to bud
    direction = bud_center - center
    direction = direction / np.linalg.norm(direction)

    # Create cylinder for neck
    cylinder = pv.Cylinder(
        center=(center + bud_center) / 2,  # Midpoint
        direction=direction,
        radius=neck_radius,
        height=bud_distance,
    )

    # Combine shapes using boolean operations
    # First combine mother and neck
    mother_and_neck = mother.boolean_union(cylinder)

    # Then add the bud
    complete_cell = mother_and_neck.boolean_union(bud)

    # Clean up the mesh
    complete_cell = complete_cell.clean()
    complete_cell = complete_cell.fill_holes(1)

    # Verify mesh integrity
    edges = complete_cell.extract_feature_edges(
        feature_edges=False, manifold_edges=False
    )
    assert edges.n_cells == 0, "Mesh has non-manifold edges"

    return BuddingCell(
        mesh=complete_cell,
        center=center,
        mother_radius_x=mother_radius_x,
        mother_radius_y=mother_radius_y,
        mother_radius_z=mother_radius_z,
        bud_radius_x=bud_radius_x,
        bud_radius_y=bud_radius_y,
        bud_radius_z=bud_radius_z,
        bud_angle=bud_angle,
        bud_distance=bud_distance,
        neck_radius=neck_radius,
    )