InteractiveViewerUsage.md

10 minutes to interactive-viewer

Welcome to interactive-viewer!

interactive-viewer is a web application for interactively 3D reconstruction of spatial transcriptomics in 3D space.

How to use

Installation

You can clone the Spateo-Viewer with git and install dependencies with pip:

git clone https://github.com/aristoteleo/spateo-viewer.git
cd spateo-viewer
pip install -r requirements.txt

Running (Users could change the port)

python stv_interactive_app.py --port 1234

How to generate the anndata object to upload

import spateo as st

# Load the anndata object
adata = st.read_h5ad("E7_8h_cellbin.h5ad")

# Make sure adata.obsm contains 'spatial' to save the coordinates
adata.obsm['spatial'] = adata.obsm['3d_align_spatial']

# Interactive-viewer will read all info contained in anndata.obs, so please make sure the info you need has been saved in anndata.obs

# Save the anndata object
 adata.write_h5ad("E7_8h_cellbin.h5ad", compression="gzip")

You can refer to the data structure we include by default in the dataset.

How to upload data

1. Upload file via the tool included in the toolbar in the web application:

   

2. Upload folder via the stv_interactive_app.py:

   from stviewer.interactive_app import interactive_server, state
   
   if __name__ == "__main__":
     **state.upload_anndata = None**
     interactive_server.start()
   

   Change None in state.upload_anndata = None to the absolute path of the file you want to upload.(Please give priority to this method when used in remote servers)