Segger: Reproducible Analyses for Fast and Accurate Cell Segmentation in Imaging-Based Spatial Omics
This repository contains code and analyses for reproducing figures in the preprint Segger: Fast and accurate cell segmentation of imaging-based spatial omics data. Segger is a graph-based segmentation framework that improves transcript assignment in spatial omics data while offering high sensitivity, specificity, and scalability.
notebooks_share/
– Jupyter notebooks for reproducing figures and performing key analyses.src/
– Python modules for data preprocessing, visualization, and utility functions.
The datasets used in this study are publicly available and can be accessed as follows:
- Xenium Breast Cancer Dataset:
Download (tar) - Xenium Colon Dataset:
Download (tar.gz) - Xenium NSCLC Dataset:
Download (tar.gz)
- Xenium Breast Cancer (10x Genomics):
Dataset Link - Xenium Colon (10x Genomics):
Dataset Link
Download the datasets Run the following commands to download and extract the datasets:
wget https://dp-lab-data-public.s3.us-east-1.amazonaws.com/segger/xenium_breast.tar
wget https://dp-lab-data-public.s3.us-east-1.amazonaws.com/segger/xenium_colon.tar.gz
wget https://dp-lab-data-public.s3.us-east-1.amazonaws.com/segger/xenium_nsclc.tar.gz
tar -xvf xenium_breast.tar
tar -xvzf xenium_colon.tar.gz
tar -xvzf xenium_nsclc.tar.gz
For questions or issues, please open a GitHub issue or contact the authors of the manuscript.