spotiphy

library0.3.1pypypiunverified

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

ai-ml data

pip install spotiphy

github ↗package ↗

INSTALL

IMPORT

SIG · SPOTIPHY

spotiphy

ai-mlpythonv0.3.1

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

Spotiphy

✓ from spotiphy import Spotiphy

✗ import spotiphy

Direct import of module does not give easy access to the main class.

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()

Debug

Known issues

gotchaThe 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).

affects: all

deprecatedOlder 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.

affects: <0.2.0

Upgrade

Version history

0.3.1latest on PyPI · released Oct 3, 2025

Audit

Dependencies

No dependency data recorded yet.

Agent activity

9 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/jyyulab/Spotiphy ↗

packagehttps://pypi.org/project/spotiphy/ ↗