xenium_NAC

NAc A-P

Welcome to the NAc A-P project repository! Here you will find all code used to analyze the data generated as part of the manuscript “Three dimensional reconstruction of the human nucleus accumbens reveals topographic organization and molecular heterogeneity of D1-islands across the anterior posterior axis”.

IMPORTANT NOTE: Some pdf/png versions of plots generated in the analysis were not pushed to the repository to avoid the inclusion of very large files.

Study Design

This study performs deep anatomical profiling of the human nucleus accumbens (NAc) via Xenium spatial transcriptomics. Specifically, we performed Xenium on 11 sequential sections separated by ~500um across, 2 donors for a total of 22 sections. We also performed VisiumHD, a single cell resolution spatial Transcriptomics technology, across 8 arrays and specifically targeted anatomical regions containing D1-islands. Following collection of all data, we present a three-dimensional reconstruction of the human NAc across the anterior posterior technology.

Citing our work

Please cite this (manuscript if you use data from this project.

Robert A. Phillips III, Jianing Yao, Svitlana V. Bach, Ishbel Del Rosario Alvia, Yufeng Du, Sarah E. Maguire, Ruth Zhang, Ryan A. Miller, Joel E. Kleinman, Thomas M. Hyde, Keri Martinowich, Kristen R. Maynard, Stephanie C. Hicks. Three dimensional reconstruction of the human nucleus accumbens reveals topographic organization and molecular heterogeneity of D1-islands across the anterior posterior axis. bioRxiv [Preprint]. 2026 UPDATE DATE. doi: UPDATE DOI. PMID: UPDATE PMID; PMCID: UPDATE PMCID.

Below is the citation in BibTeX format.

@article{phillipsya2026,
  title={Three dimensional reconstruction of the human nucleus accumbens reveals topographic organization and molecular heterogeneity of D1-islands across the anterior posterior axis},
  author={Robert A. Phillips III, Jianing Yao, Svitlana V. Bach, Ishbel Del Rosario Alvia, Yufeng Du, Sarah E. Maguire, Ruth Zhang, Ryan A. Miller, Joel E. Kleinman,  Thomas M. Hyde, Keri Martinowich, Kristen R. Maynard, Stephanie C. Hicks. },
  journal={bioRxiv},
  year={2026},
  publisher={Cold Spring Harbor Laboratory Preprints}
  }

Interactive Websites

All of these interactive websites are powered by open source software, namely:

• 🔍 samui
• 👀 iSEE

We provide the following interactive websites, organized by dataset with software labeled by emojis:

• Shiny App
  • 🔍 VisiumHD shiny app
• Samui
  • 🔍 Samui: 2 Donors - 11 samples per donor
• 3D Reconstruction links
  • 🔍 D1 Island B reconstruction
  • 🔍 D1 Island A reconstruction
  • 🔍 D1 Island A B reconstruction
  • 🔍 WM reconstruction

Data Access

Zenodo Archive for this project can be found at 10.5281/zenodo.22755736. Project data was also uploaded to the NeMO and can be found at nemo:col-s93bogv.

Contact

We value public questions, as they allow other users to learn from the answers. If you have any questions, please ask them at LieberInstitute/xenium_NAC/issues and refrain from emailing us. Thank you again for your interest in our work!