Note

This page was generated from Morpholoy.ipynb. Interactive online version: . Some tutorial content may look better in light mode.

Morphological features of 3D models

This notebook demonstrates the calculation of morphological features of 3D reconstructed model, including length, surface area, volume, cell density, cell distribution, etc.

import warnings
warnings.filterwarnings('ignore')
import spateo as st

2023-07-25 12:25:01.846617: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT

Load the data

cpo = [(553, 1098, 277), (1.967, -6.90, -2.21), (0, 0, 1)]

adata = st.sample_data.drosophila(filename="E7-9h_cellbin.h5ad")
adata.uns["__type"] = "UMI"
adata

AnnData object with n_obs × n_vars = 25921 × 8136
    obs: 'area', 'slices', 'anno_cell_type', 'anno_tissue', 'anno_germ_layer', 'actual_stage'
    uns: '__type'
    obsm: '3d_align_spatial'
    layers: 'counts_X', 'spliced', 'unspliced'

Reconstruct the mesh model corresponding to the 3D spatial transcriptomics data

See also 3D Reconstruction for more details on 3D reconstructed models.

# Reconstruct point cloud model
pc, plot_cmap = st.tdr.construct_pc(adata=adata.copy(), spatial_key="3d_align_spatial", groupby="anno_tissue")

# Reconstruct mesh model
mesh, _, _ = st.tdr.construct_surface(pc=pc, alpha=0.3, cs_method="marching_cube", cs_args={"mc_scale_factor": 1.8}, smooth=8000, scale_factor=1.0)

# Visualization
st.pl.three_d_plot(model=st.tdr.collect_models([pc, mesh]), key="groups", model_style=["points", "surface"], jupyter="static", cpo=cpo)

Calculate the cells’ kernel density of drosophila embryo

st.tdr.pc_KDE(pc=pc, bandwidth=5, key_added="cells_kde", colormap="hot_r", inplace=True)
st.pl.three_d_plot(model=pc, key="cells_kde", colormap="hot_r", opacity=0.6, model_style="points", jupyter="static", cpo=cpo)

Calculate the volume, surface area, length, etc. of drosophila embryo

The coordinates in anndata need a unified unit, such as all coordinates are in microns

um_pc_model, um_mesh_model = pc.copy(), mesh.copy()

um_pc_model.points = um_pc_model.points / 1000
um_mesh_model.points = um_mesh_model.points / 1000

morph = st.tdr.model_morphology(model=um_mesh_model, pc=um_pc_model)
morph

|-----> Length (x) of model: 0.54292;
|-----> Width (y) of model: 0.23302;
|-----> Height (z) of model: 0.20113;
|-----> Surface area of model: 0.3212;
|-----> Volume of model: 0.01364;
|-----> Volume / surface area ratio of model: 0.04247.
|-----> Cell density of model: 1900366.56891.

{'Length(x)': 0.54292,
 'Width(y)': 0.23302,
 'Height(z)': 0.20113,
 'Surface_area': 0.3212,
 'Volume': 0.01364,
 'V/SA_ratio': 0.04247,
 'cell_density': 1900366.56891}