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.

Repository Structure

• paper/ – Notebooks reproducing the figures of the revised manuscript, from data download to figure panels (see paper/README.md).
• notebooks_share/ – Jupyter notebooks for reproducing the figures of the preprint.
• src/ – Python modules for data preprocessing, visualization, and utility functions (sg_utils).

Associated Data

The datasets used in this study are publicly available and can be accessed as follows:

AWS-hosted datasets for this publication

• Xenium Breast Cancer Dataset:
  Download (tar)
• Xenium Colon Dataset:
  Download (tar.gz)
• Xenium NSCLC Dataset:
  Download (tar.gz)
• MERSCOPE Brain Dataset:
  Download (tar.gz)
• CosMx Pancreas Dataset:
  Download (tar.gz)
• Xenium CRC Multimodal Dataset:
  Download (tar.gz)

Publicly available IST datasets

• Xenium Breast Cancer (10x Genomics):
  Dataset Link
• Xenium Colon (10x Genomics):
  Dataset Link
• MERSCOPE Brain (Vizgen):
  Dataset Link
• CosMx Pancreas (Nanostring):
  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
wget https://dp-lab-data-public.s3.us-east-1.amazonaws.com/segger/merscope_brain.tar.gz
wget https://dp-lab-data-public.s3.us-east-1.amazonaws.com/segger/cosmx_pancreas.tar.gz
wget https://dp-lab-data-public.s3.us-east-1.amazonaws.com/segger/xenium_colon_multimodal.tar.gz

tar -xvf xenium_breast.tar
tar -xvzf xenium_colon.tar.gz
tar -xvzf xenium_nsclc.tar.gz
tar -xvzf merscope_brain.tar.gz
tar -xvzf cosmx_pancreas.tar.gz
tar -xvzf xenium_colon_multimodal.tar.gz

Contact

For questions or issues, please open a GitHub issue or contact the authors of the manuscript.