stImpute

stImpute is a novel method that leverages single-cell data to predict authentic spatial transcriptomics data by integrating gene relationships. stImpute initiates the process using an autoencoder to create joint embeddings of spatial and single-cell transcriptomics data. These embeddings are then used to identify the nearest neighboring cells in scRNA-seq data for each cell in the spatial transcriptomics dataset. Subsequently, stImpute predicts spatial gene expression for each spatial cell using the nearest neighboring cells through a graph neural network (GNN), where nodes represent genes. The gene-to-gene relationships in the GNN are based on cosine similarity, utilizing the pre-trained embeddings of the gene-encoding proteins extracted from the protein language model ESM-2. In addition, stImpute is capable of identifying genes that efficiently predict imputation uncertainty, allowing the method to select genes that are reliably imputed.

Installation

We recommend using Anaconda to create a new Python environment and activate it via

conda env create -f stImpute_env.yaml
conda activate stImpute_env

Quick Start

Input

• spatial_df: [pandas dataframe] normalized and logarithmized original spatial data (cell by gene)
• scrna_df: [pandas dataframe] normalized and logarithmized reference scRNA-seq data (cell by gene)
• train_gene: [numpy array] genes for training
• test_gene: [numpy array] genes for predicting
• seed: [int] random seed in torch
• emb_file: [str] a file containing the results of gene's coding by ESM-2 (or None)

Output

• stImpute_res: [pandas dataframe] predicted spatial data (cell by gene)
• reliable_score: [numpy array] predicted gene's reliable score

For calling stImpute programmatically

stImpute_res, reliable_score = stImpute(spatial_df, scrna_df, train_gene, test_gene, seed=seed, emb_file=emb_file)

Reproduce the result of the paper

Main result

1. Change lines 17-19 of train.py to the address of the dataset you downloaded(The download address for the dataset will be provided later)

st_adata = sc.read_h5ad('dataset/st-seq/osmFISH.h5ad')
sc_adata = sc.read_h5ad('dataset/scRNA-seq/Zeisel.h5ad')
emb_file = 'embed/osmFISH_emb.pkl'

2. Run train.py

python train.py

If you want to accurately reproduce the results in the paper, use NVIDIA GeForce RTX 4090

The other result

We provide the full reproduction process here of the other result in the paper(The address will be provided later)

Tutorial

Spatial transcriptomic data impute

1. Install the required environment according to stImpute Installation.

2. Get the ESM-2 embedding for the genes associated with your dataset.

   If you don't want to get the embedding, you can skip this step and set emb_file = None in the next step.

3. Change lines 17-19 of train.py to the address and the embedding of your dataset.

st_adata = sc.read_h5ad('st_seq_data.h5ad')
sc_adata = sc.read_h5ad('scRNA_seq_data.h5ad')
emb_file = 'emb.pkl' # or set emb_file = None

4. Run train.py

python train.py

You can also run the tutorial tutorial.ipynb for more detailed information.