ImputeFISH 0.0.2

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

# 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 `