pysodb is a python package that provides the interface to access the data in SODB.
- Clone the source code.
git clone https://github.com/TencentAILabHealthcare/pysodb.git
cd pysodb
- Create a conda environment and activate it.
conda env create -n pysodb --file pysodb.yml
conda activate pysodb
- Install pysodb as a dependency or third-party package with pip:
pip install .
import pysodb
sodb = pysodb.SODB() # Initialization
dataset_list = sodb.list_dataset() # Get the list of datasets
dataset_list = sodb.list_dataset_by_category() # Get the list of datasets with specific category. categories ["Spatial Transcriptomics", "Spatial Proteomics", "Spatial Metabolomics", "Spatial Genomics", "Spatial MultiOmics"]
adata = sodb.load_experiment('hunter2021spatially','sample_B') # Load a specific experiment
adataset = sodb.load_dataset('hunter2021spatially') # Load a specific dataset
Please refer to 📘Documentation and Tutorials for more details. We also provided step-by-step protocols to integrate Pysodb and various spatial omics analysis tools, please refer to 📘Protocols for more details.
Yuan, Z., Pan, W., Zhao, X. et al. SODB facilitates comprehensive exploration of spatial omics data. Nat Methods (2023). https://doi.org/10.1038/s41592-023-01773-7
Lin, S., Zhao, F., Wu, Z. et al. Streamlining spatial omics data analysis with Pysodb. Nat Protoc (2023). https://doi.org/10.1038/s41596-023-00925-5