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Introduction

This repository contains software and pre-processed data for analyzing spatial transcriptomics.

Requirement

  1. Python 3.7 with numpy, pandas, and matplotlib
  2. OpenCV
  3. tqdm

Setup

Run the following command in src to extract the region of interest in the image:

python every_breast_tumor.py

Data

We included sample pre-processed roi image for covenience. Raw data from https://support.10xgenomics.com/spatial-gene-expression/datasets/1.0.0/V1_Breast_Cancer_Block_A_Section_1. We include the pre-processing script; these can be modified as required.