fix: add volume functions for Corning 96-well flat and V-bottom plates

pylabrobot/resources/corning/plates.py

@@ -1,8 +1,12 @@
 """ Corning plates. """
 
 from pylabrobot.resources.height_volume_functions import (
+  calculate_liquid_height_in_container_2segments_round_vbottom,
   calculate_liquid_height_in_container_2segments_square_vbottom,
+  calculate_liquid_volume_container_2segments_round_vbottom,
   calculate_liquid_volume_container_2segments_square_vbottom,
+  compute_height_from_volume_conical_frustum_in_well,
+  compute_volume_from_height_conical_frustum_in_well,
 )
 from pylabrobot.resources.plate import Lid, Plate
 from pylabrobot.resources.utils import create_ordered_items_2d
@@ -35,6 +39,12 @@ def Cor_96_wellplate_360ul_Fb(name: str, with_lid: bool = False) -> Plate:
 
   # This used to be Cos_96_EZWash in the Esvelt lab
 
+  # Corning MicroplateDimensions96-384-1536.pdf:
+  # top internal diameter 6.86mm, bottom internal diameter 6.35mm, well depth 10.67mm
+  BOTTOM_RADIUS = 6.35 / 2
+  TOP_RADIUS = 6.86 / 2
+  WELL_DEPTH = 10.67
+
   return Plate(
     name=name,
     size_x=127.76,
@@ -53,11 +63,21 @@ def Cor_96_wellplate_360ul_Fb(name: str, with_lid: bool = False) -> Plate:
       item_dy=9.0,
       size_x=6.86,  # top
       size_y=6.86,  # top
-      size_z=10.67,
+      size_z=WELL_DEPTH,
       material_z_thickness=0.5,
       bottom_type=WellBottomType.FLAT,
       cross_section_type=CrossSectionType.CIRCLE,
       max_volume=360,
+      compute_volume_from_height=lambda liquid_height: (
+        compute_volume_from_height_conical_frustum_in_well(
+          liquid_height, BOTTOM_RADIUS, TOP_RADIUS, WELL_DEPTH
+        )
+      ),
+      compute_height_from_volume=lambda liquid_volume: (
+        compute_height_from_volume_conical_frustum_in_well(
+          liquid_volume, BOTTOM_RADIUS, TOP_RADIUS, WELL_DEPTH
+        )
+      ),
     ),
   )
 
@@ -82,6 +102,75 @@ def Cos_96_EZWash(name: str, with_lid: bool = False) -> Plate:
   raise ValueError("Deprecated. You probably want to use Cor_96_wellplate_360ul_Fb instead.")
 
 
+# # # # # # # # # # Cor_96_wellplate_320ul_Vb # # # # # # # # # #
+
+
+def Cor_96_wellplate_320ul_Vb(name: str, with_lid: bool = False) -> Plate:
+  """
+  Corning cat. no.s: 3894, 3896, 3897, 3898, 3342
+  - manufacturer_link: https://ecatalog.corning.com/life-sciences/b2c/US/en/Microplates/
+    Assay-Microplates/96-Well-Microplates/Corning%C2%AE-96-well-Clear-Polystyrene-Microplates/p/3894
+  - brand: Corning / Costar
+  - material: Polystyrene
+  - notes:
+      - Standard 96-well V-bottom microplate.
+      - Well geometry: conical V-bottom section (cone height ~1.6mm) transitioning to a
+        cylindrical section. Dimensions from Corning MicroplateDimensions96-384-1536.pdf:
+        top internal diameter 6.86mm, bottom internal diameter 6.37mm, well depth 11.12mm,
+        total well volume 320uL.
+  """
+
+  # Corning MicroplateDimensions96-384-1536.pdf:
+  # top internal diameter 6.86mm, bottom internal diameter 6.37mm, well depth 11.12mm
+  # The V-bottom is modeled as a cone (apex at bottom) transitioning to a cylinder.
+  # Cone height back-calculated from published total volume (320uL) using d=6.37mm.
+  WELL_DIAMETER = 6.37  # diameter at cone-to-cylinder transition
+  CONE_HEIGHT = 1.62  # mm, back-calculated to match 320uL total volume
+  CYLINDER_HEIGHT = 11.12 - CONE_HEIGHT  # 9.50mm
+  WELL_DEPTH = 11.12
+
+  return Plate(
+    name=name,
+    size_x=127.76,
+    size_y=85.48,
+    size_z=14.2,
+    lid=Cor_96_wellplate_320ul_Vb_Lid(name=name + "_lid") if with_lid else None,
+    model="Cor_96_wellplate_320ul_Vb",
+    ordered_items=create_ordered_items_2d(
+      Well,
+      num_items_x=12,
+      num_items_y=8,
+      dx=10.87,  # 14.3-6.86/2
+      dy=7.77,  # 11.2-6.86/2
+      dz=2.58,  # 14.2 - 11.12 - 0.5
+      item_dx=9.0,
+      item_dy=9.0,
+      size_x=6.86,
+      size_y=6.86,
+      size_z=WELL_DEPTH,
+      material_z_thickness=0.5,
+      bottom_type=WellBottomType.V,
+      cross_section_type=CrossSectionType.CIRCLE,
+      compute_volume_from_height=lambda liquid_height: (
+        calculate_liquid_volume_container_2segments_round_vbottom(
+          d=WELL_DIAMETER, h_cone=CONE_HEIGHT, h_cylinder=CYLINDER_HEIGHT,
+          liquid_height=liquid_height,
+        )
+      ),
+      compute_height_from_volume=lambda liquid_volume: (
+        calculate_liquid_height_in_container_2segments_round_vbottom(
+          d=WELL_DIAMETER, h_cone=CONE_HEIGHT, h_cylinder=CYLINDER_HEIGHT,
+          liquid_volume=liquid_volume,
+        )
+      ),
+    ),
+  )
+
+
+def Cor_96_wellplate_320ul_Vb_Lid(name: str) -> Lid:
+  raise NotImplementedError("This lid is not currently defined.")
+
+
 # # # # # # # # # # Cor_96_wellplate_2mL_Vb # # # # # # # # # #
 
 

pylabrobot/resources/height_volume_functions.py

@@ -559,6 +559,72 @@ def compute_height_from_volume_conical_frustum(
   )
 
 
+def compute_volume_from_height_conical_frustum_in_well(
+  liquid_height: float, bottom_radius: float, top_radius: float, total_height: float
+) -> float:
+  """Compute volume (uL) from height (mm) for liquid in a conical-frustum-shaped well.
+
+  Unlike :func:`compute_volume_from_height_conical_frustum`, this correctly interpolates the
+  radius at the liquid surface based on the fill height. In a tapered well, the cross-sectional
+  radius varies linearly from ``bottom_radius`` at h=0 to ``top_radius`` at h=total_height.
+
+  Args:
+    liquid_height: Height of the liquid in mm.
+    bottom_radius: Inner radius at the bottom of the well in mm.
+    top_radius: Inner radius at the top of the well in mm.
+    total_height: Total internal height of the well in mm.
+
+  Returns:
+    Volume of liquid in uL (= mm^3).
+  """
+  if liquid_height <= 0:
+    return 0.0
+  h = min(liquid_height, total_height)
+  r_at_h = bottom_radius + (top_radius - bottom_radius) * h / total_height
+  return (math.pi * h / 3.0) * (r_at_h**2 + r_at_h * bottom_radius + bottom_radius**2)
+
+
+def compute_height_from_volume_conical_frustum_in_well(
+  liquid_volume: float, bottom_radius: float, top_radius: float, total_height: float
+) -> float:
+  """Compute height (mm) from volume (uL) for liquid in a conical-frustum-shaped well.
+
+  Inverse of :func:`compute_volume_from_height_conical_frustum_in_well`. Uses binary search
+  because the volume-height relationship is cubic (not analytically invertible in closed form).
+
+  Args:
+    liquid_volume: Volume of the liquid in uL (= mm^3).
+    bottom_radius: Inner radius at the bottom of the well in mm.
+    top_radius: Inner radius at the top of the well in mm.
+    total_height: Total internal height of the well in mm.
+
+  Returns:
+    Height of the liquid in mm.
+  """
+  if liquid_volume <= 0:
+    return 0.0
+
+  max_volume = compute_volume_from_height_conical_frustum_in_well(
+    total_height, bottom_radius, top_radius, total_height
+  )
+  if liquid_volume > max_volume:
+    raise ValueError(
+      f"Volume {liquid_volume} exceeds maximum well volume {max_volume:.2f}."
+    )
+
+  low, high = 0.0, total_height
+  tolerance = 1e-6
+  while high - low > tolerance:
+    mid = (low + high) / 2
+    if compute_volume_from_height_conical_frustum_in_well(
+      mid, bottom_radius, top_radius, total_height
+    ) < liquid_volume:
+      low = mid
+    else:
+      high = mid
+  return (low + high) / 2
+
+
 def compute_volume_from_height_square(liquid_height: float, well_side_length: float) -> float:
   """Compute volume (uL) from height (mm) for a square well."""
   return liquid_height * (well_side_length**2)