Metadata-Version: 2.4
Name: ImputeFISH
Version: 0.0.6
Summary: ImputeFISH: A Spatially Aware and Scalable Framework for Gene Imputation in Imaging-Based Spatial Transcriptomics
Home-page: https://github.com/swainasish/ImputeFISH
Author: Asish Kumar Swain
Author-email: swainkasish@gmail.com
License: MIT
Keywords: willupdate
Classifier: Development Status :: 5 - Production/Stable
Classifier: Operating System :: Microsoft :: Windows :: Windows 10
Classifier: Operating System :: POSIX :: Linux
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
License-File: LICENCE.txt
Requires-Dist: scikit-learn>=1.7.2
Requires-Dist: scipy>=1.15.3
Requires-Dist: seaborn>=0.13.2
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: home-page
Dynamic: keywords
Dynamic: license
Dynamic: license-file
Dynamic: requires-dist
Dynamic: summary

# ImputeFISH

**ImputeFISH: A Spatially Aware and Scalable Framework for Gene Imputation in Imaging-Based Spatial Transcriptomics**

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## 🔍 Overview

**ImputeFISH** (*Imputation for Fluorescence In-Situ Hybridization–based spatial transcriptomics*) is a spatially aware and scalable framework designed for **gene imputation** and **atlas-scale transcriptome enhancement** in imaging-based spatial transcriptomics (IST) datasets such as MERFISH, Xenium, and seqFISH.

ImputeFISH integrates spatial context and scRNA-seq references to recover unmeasured genes, enabling more complete transcriptome representations and improved biological interpretation.

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## 🚀 Key Features

- 🧠 **Reference Selection:** Automatically identifies the most compatible scRNA-seq reference using a **gene co-expression network–based compatibility filter**.  
- 🌐 **Spatial Awareness:** Incorporates neighborhood-level spatial information inspired by **graph neural network message passing**.  
- 🔄 **Domain Adaptation:** Applies **SVD-based domain alignment** to correct batch effects between IST and scRNA-seq datasets.  
- ⚡ **Scalability:** Efficiently scales to **millions of cells**, suitable for atlas-scale datasets.  
- 🧬 **Accurate Gene Imputation:** Uses **non-negative ridge regression** to predict unmeasured gene expression.  

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## 📦 Installation

You can install **ImputeFISH** using pip:

```bash
pip install imputefish
```
