3D reconstructions of liver, heart, and a brain subregion that varies along the left-right axis

import pandas as pd
import numpy as np
import scanpy as sc
import anndata as ad
import umap
import os
import scipy.sparse
import matplotlib.pyplot as plt
from matplotlib.cm import get_cmap
import matplotlib as mpl

import warnings
warnings.filterwarnings("ignore")

Load results

# load 3d spatial locations
n_slice = 5
res_path = "Results/INSPIRE_3d_reconstruction"
adata_st_list = []
for i in range(n_slice):
    adata = sc.read_h5ad(res_path + "/adata_3d_spatial_"+str(i)+".h5ad")
    adata_st_list.append(adata)

rgb_10 = [i for i in get_cmap('Set3').colors]
rgb_20 = [i for i in get_cmap('tab20').colors]
rgb_20b = [i for i in get_cmap('tab20b').colors]
rgb_dark2 = [i for i in get_cmap('Dark2').colors]
rgb_pst1 = [i for i in get_cmap('Pastel1').colors]
rgb_acc = [i for i in get_cmap('Accent').colors]
rgb2hex_10 = [mpl.colors.rgb2hex(color) for color in rgb_10]
rgb2hex_20 = [mpl.colors.rgb2hex(color) for color in rgb_20]
rgb2hex_20b = [mpl.colors.rgb2hex(color) for color in rgb_20b]
rgb2hex_20b_new = [rgb2hex_20b[i] for i in [0, 3, 4, 7, 8, 11, 12, 15, 16, 19]]
rgb2hex_dark2 = [mpl.colors.rgb2hex(color) for color in rgb_dark2]
rgb2hex_pst1 = [mpl.colors.rgb2hex(color) for color in rgb_pst1]
rgb2hex_acc = [mpl.colors.rgb2hex(color) for color in rgb_acc]
rgb2hex = rgb2hex_20 + rgb2hex_20b_new + rgb2hex_dark2 + rgb2hex_pst1 + rgb2hex_acc

Liver

louvain_id = "3"

fig = plt.figure(figsize=(8,8))
ax = fig.add_subplot(111, projection='3d')

size = .05

# draw slices
for i_slice in range(n_slice):
    ax.scatter(adata_st_list[i_slice].obsm["spatial_3d"][:,0],
               adata_st_list[i_slice].obsm["spatial_3d"][:,1],
               adata_st_list[i_slice].obsm["spatial_3d"][:,2], s=0.03, c="gray", alpha=0.1)

# draw regions
for i_slice in range(n_slice):
    ad_tmp = adata_st_list[i_slice][adata_st_list[i_slice].obs["louvain"].values.astype(str) == louvain_id, :]
    ax.scatter(ad_tmp.obsm["spatial_3d"][:,0],
               ad_tmp.obsm["spatial_3d"][:,1],
               ad_tmp.obsm["spatial_3d"][:,2], s=size, c=rgb2hex[3], alpha=1)

plt.show()

Heart

louvain_id = "12"

fig = plt.figure(figsize=(8,8))
ax = fig.add_subplot(111, projection='3d')

size = .05

# draw slices
for i_slice in range(n_slice):
    ax.scatter(adata_st_list[i_slice].obsm["spatial_3d"][:,0],
               adata_st_list[i_slice].obsm["spatial_3d"][:,1],
               adata_st_list[i_slice].obsm["spatial_3d"][:,2], s=0.03, c="gray", alpha=0.1)

# draw regions
for i_slice in range(n_slice):
    ad_tmp = adata_st_list[i_slice][adata_st_list[i_slice].obs["louvain"].values.astype(str) == louvain_id, :]
    ax.scatter(ad_tmp.obsm["spatial_3d"][:,0],
               ad_tmp.obsm["spatial_3d"][:,1],
               ad_tmp.obsm["spatial_3d"][:,2], s=size, c=rgb2hex[12], alpha=1)

plt.show()

The brain subregion which varies along the left-right axis

louvain_id = "13"

fig = plt.figure(figsize=(8,8))
ax = fig.add_subplot(111, projection='3d')

size = .05

# draw slices
for i_slice in range(n_slice):
    ax.scatter(adata_st_list[i_slice].obsm["spatial_3d"][:,0],
               adata_st_list[i_slice].obsm["spatial_3d"][:,1],
               adata_st_list[i_slice].obsm["spatial_3d"][:,2], s=0.03, c="gray", alpha=0.1)

# draw regions
for i_slice in range(n_slice):
    ad_tmp = adata_st_list[i_slice][adata_st_list[i_slice].obs["anno"].values.astype(str) == louvain_id, :]
    ax.scatter(ad_tmp.obsm["spatial_3d"][:,0],
               ad_tmp.obsm["spatial_3d"][:,1],
               ad_tmp.obsm["spatial_3d"][:,2], s=size, c=rgb2hex[13], alpha=1)

plt.show()