SEU-3D-tool

Tool for building SEU-3D-like spatial-temporal omics web browser.

Installation

It's recommended to install the seu3d-tool in a conda enviroment.

conda create -n seu3d python=3.11
conda activate seu3d
pip install seu3d-tool

Deployment

Server configuration

If you don't have a config file, you should first generate one use:

# Generating a configuration file named `seu3d_config.yaml` in current directory.
seu3d-tool config --new

The configuration file seu3d_config.yaml looks like:

# -------
# data to show on the server, in .h5ad format
# a unique name for each file, and the path to the file
# e.g. 
# Dataset:
#   E7.5: /path/to/E7.5.h5ad
#   E8.0: /path/to/E8.0.h5ad
Dataset:

# -------
# name for the celltype annotation stored in the .h5ad files (adata.obs[annotation]), default: 'celltype'
annotation: celltype

# -------
# name for the 3D embedding stored in the .h5ad files (adata.obsm[3D_embedding]), default: 'X_spatial'
3D_embedding: X_3D

# -------
# dir to store cache files, default: './cache'
cache_dir: ./cache

# -------
# colormap:
# Colormap will be auto generated when first startup. After that, you could use
# 'seu3d-tool config --current > seu3d_config.yaml' to get updated config file and modify the colormap,
# and use 'seu3d-tool config --update seu3d_config.yaml' to update server configuration.

You should fill all the configuration items except the colormap (server will auto generate it). Then you could update the server configuration use:

seu3d-tool config --update seu3d_config.yaml

If you want to check the current configuration, you could use:

seu3d-tool config --current

It will print the current configuration file of server, you could export it to a file and modify it.

seu3d-tool config --current > seu3d_config.yaml

Start the server

Now the configuration is completed, you could start the server by:

seu3d-tool

If you want to change the port(default: 8050) and host (default: 0.0.0.0) of the server, you could start it with some extra parameters:

seu3d-tool --port=8051 --host=xxx.xx.xx.x

Customized colormap

For each unique cell type annotation of all the data in dataset, a initial color will be assigned. The the colormap will be stored into server configuration after server startup, you could get the updated configuration file and customize the colormap by yourself.

seu3d-tool config --current > seu3d_config.yaml
vim seu3d_config.yaml
seu3d-tool config --update seu3d_config.yaml

Usage

Tutorial: https://rainyblue-w.github.io/SEU-3D/