CSHL Single Cell Biology Core
Spatial Biology Club
June 2024
Speakers:
​
Jon Preall
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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:
SpatialData ​
​​​​
October 2024
Andrew Ji
​
Probing the single-cell spatial transcriptomic landscape of human skin across anatomic sites
December 2024
Li Yuan​
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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
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Nischal Bhandari​
Resolving the Spatial Dynamics of Early Cancer Progression
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September 2025
Huaien Wang​
Exploring PDAC with Xenium
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The Space Team​
What's New with the Lunaphore COMET (Multiplexed IF)
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