CSHL Single Cell Biology Core
Spatial Biology Club
June 2024
Speakers:
Jon Preall
Spatial 'Omics at the Single Cell Core
Claire Regan
Getting Started with Visium
General Resources and Tutorials:
Awesome Spatial Omics Github and Awesome Single Cell Github
Guidebook of Spatial Transcriptomics Review
Best Practices for Spatial Transcriptomics Analysis with Bioconductor
Some packages to check out:
R Packages:
Python Packages:
stLearn (requires python 3.8 which can make it a bit challenging to include in an environment)
Next
Meeting:
See you in 2026
Upcoming Meetings:
July 2024
Speakers:
Jon Preall
Xenium at the Single Cell Core
Anita Ng
Exploring CLL with CellDive and Halo
General Resources and Tutorials:
Awesome Spatial Omics Github and Awesome Single Cell Github
Guidebook of Spatial Transcriptomics Review
Best Practices for Spatial Transcriptomics Analysis with Bioconductor
Some packages to check out:
R Packages:
Python Packages:
stLearn (requires python 3.8 which can make it a bit challenging to include in an environment)
Other tools:
August 2024
Bring Your Own Data Workshop
September 2024
Speakers:
Claire Regan
Visium HD ABCs: Artifacts, Binning and Cell Typing
Andrew Shih
Annotating Tissue Architecture with HALO AI
General Resources and Tutorials:
Awesome Spatial Omics Github and Awesome Single Cell Github
Guidebook of Spatial Transcriptomics Review
Best Practices for Spatial Transcriptomics Analysis with Bioconductor
Some packages to check out:
R Packages:
Python Packages:
October 2024
Andrew Ji
Probing the single-cell spatial transcriptomic landscape of human skin across anatomic sites
December 2024
Li Yuan
High-Throughput Neural Projection Mapping with Axonal BARseq: Exploring Methodology and Analysis
June 2025
Jon Preall
How to Run 40-plex IF at the Core with Lunaphore COMET
July 2025
Alex Harris
Optimizing Multiplexed IF on the Aging Mouse Brain
Nischal Bhandari
Resolving the Spatial Dynamics of Early Cancer Progression
September 2025
Huaien Wang
Exploring PDAC with Xenium
The Space Team
What's New with the Lunaphore COMET (Multiplexed IF)
