Spotiphy

0.3.1 verified Sat May 09 auth: no python

Integrated pipeline for spatial transcriptomics deconvolution and decomposition to generate pseudo single-cell resolution images. Current version 0.3.1, active development on GitHub.

pip install spotiphy

Common errors

error ModuleNotFoundError: No module named 'spotiphy' ↓

cause Library not installed or installed in wrong environment.

fix

Run pip install spotiphy in the correct Python environment (Python >=3.9).

error AttributeError: module 'spotiphy' has no attribute 'Spotiphy' ↓

cause Incorrect import; using `import spotiphy` instead of `from spotiphy import Spotiphy`.

fix

Use from spotiphy import Spotiphy.

Warnings

gotcha The set_dataset method expects a folder path and an h5ad file; incorrect paths or missing files cause obscure errors. ↓

fix Ensure the spatial folder contains the required spatial metadata (e.g., tissue_positions_list.csv, scalefactors_json.json).

deprecated Older versions (0.1.x) had different API (e.g., `spotiphy.SpotiFlow`). Import path changed in 0.2.0. ↓

fix Use `from spotiphy import Spotiphy` instead of old imports.

Install

pip install git+https://github.com/jyyulab/Spotiphy.git

Imports

Spotiphy
wrong
```
import spotiphy
```
correct
```
from spotiphy import Spotiphy
```
Direct import of module does not give easy access to the main class.

Quickstart

Basic usage: load Spotiphy class, set dataset, and run.

from spotiphy import Spotiphy

# Initialize with default parameters
sp = Spotiphy()

# Set required files (paths must exist)
sp.set_dataset('spatial_folder', 'counts.h5ad')

# Run pipeline
sp.run()