3D spatially-resolved gene expression patterns

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

Load results

slice_name_list = ["E16.5_E2S8", "E16.5_E2S9", "E16.5_E2S10", "E16.5_E2S11", "E16.5_E2S12"]
n_slice = len(slice_name_list)

adata_st_list = []
for i in range(n_slice):
    data_dir = "data_3d/Stereoseq-mouse-embryo/node_features_all_E16.5"
    adata = sc.read_h5ad(os.path.join(data_dir, "raw_counts/"+slice_name_list[i]+".h5ad"))
    adata.obs.index = adata.obs.index + "-" + str(i)
    adata_st_list.append(adata)

loc3d_path = "Results/INSPIRE_3d_reconstruction"
for i in range(n_slice):
    ad_3d = sc.read_h5ad(loc3d_path+"/adata_3d_spatial_"+str(i)+".h5ad")
    ad_3d = ad_3d[adata_st_list[i].obs.index, :]
    adata_st_list[i].obsm["spatial_3d"] = ad_3d.obsm["spatial_3d"]

3D expression of gene Afp in liver

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], rasterized=True,
               s=size, c=np.array(adata_st_list[i_slice][:,"Afp"].X.toarray()).reshape(-1), alpha=0.2,
               cmap="Blues", vmax=35, vmin=-1)

plt.show()

3D expression of gene Myl7 in heart

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], rasterized=True,
               s=size, c=np.array(adata_st_list[i_slice][:,"Myl7"].X.toarray()).reshape(-1), alpha=0.2,
               cmap="Blues", vmax=10, vmin=-1)

plt.show()

3D expression of gene Neurod6 in brain

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], rasterized=True,
               s=size, c=np.array(adata_st_list[i_slice][:,"Neurod6"].X.toarray()).reshape(-1), alpha=0.2,
               cmap="Blues", vmax=15, vmin=-1)

plt.show()