spatial

Last updated on Tue, May 9, 2023
#Visium_SPG_AD #spatialDLPFC #spatialLIBD spatialLIBD shiny app spatialLIBD at Bioconductor
Image credit: bioRxiv

In February 2020 we published the first pre-print using the 10x Genomics Visium platform for spatial transcriptomics. For this project we created the spatialLIBD Bioconductor package and started developing new analytical methods for this type of data. Given that we shared all the data and code when we posted the pre-print, by the time the peer-reviewed publication was made public in February 2021, others had already used our dataset to develop and showcase their methods. For example, BayesSpace’s pre-print was posted on September 2020, prior to their own June 2021 peer-reviewed publication. We are now using BayesSpace in our projects. This is an example of how open science and open access accelerate science.

spatial HumanPilot spatialLIBD VistoSeg spatialDLPFC Visium_SPG_AD scRNAseq Visium
Leonardo Collado-Torres
Leonardo Collado-Torres
Investigator @ LIBD, Assistant Professor, Department of Biostatistics @ JHBSPH

#rstats @Bioconductor/🧠 genomics @LieberInstitute/@lcgunam @jhubiostat @jtleek @andrewejaffe alumni/@LIBDrstats @CDSBMexico co-founder

Posts

HumanPilot: first spatially-resolved transcriptomics study using Visium
Would you prefer a video walkthrough over reading this blog post? Check out this explainer video 🎥 A few years ago now (2021) we published a study we refer to with a very generic name: HumanPilot (Maynard, Collado-Torres, Weber, Uytingco et al.
Last updated on Sat, May 25, 2024 13 min read Science, LIBD
Project

Publications

Integrating gene expression and imaging data across Visium capture areas with visiumStitched
Background Visium is a widely-used spatially-resolved transcriptomics assay available from 10x Genomics. Standard Visium capture areas …
Cite Project DOI Preprint Code Bioconductor
Integrating gene expression and imaging data across Visium capture areas with visiumStitched
A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex
The molecular organization of the human neocortex historically has been studied in the context of its histological layers. However, …
Cite Project DOI Preprint Code snRNA-seq code Documentation
A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex
The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics
Norepinephrine (NE) neurons in the locus coeruleus (LC) make long-range projections throughout the central nervous system, playing …
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The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics
escheR: Unified multi-dimensional visualizations with Gestalt principles
The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are …
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escheR: Unified multi-dimensional visualizations with Gestalt principles
Spatiotemporal analysis of gene expression in the human dentate gyrus reveals age-associated changes in cellular maturation and neuroinflammation
The dentate gyrus of the hippocampus is important for many cognitive functions, including learning, memory, and mood. Here, we …
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Spatiotemporal analysis of gene expression in the human dentate gyrus reveals age-associated changes in cellular maturation and neuroinflammation
VistoSeg: Processing utilities for high-resolution images for spatially resolved transcriptomics data
Spatially resolved transcriptomics (SRT) is a growing field that links gene expression to anatomical context. SRT approaches that use …
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VistoSeg: Processing utilities for high-resolution images for spatially resolved transcriptomics data
Influence of Alzheimer's Disease Related Neuropathology on Local Microenvironment Gene Expression in the Human Inferior Temporal Cortex
Neuropathological lesions in the brains of individuals affected with neurodegenerative disorders are hypothesized to trigger molecular …
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Influence of Alzheimer's Disease Related Neuropathology on Local Microenvironment Gene Expression in the Human Inferior Temporal Cortex
Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments
High-resolution and multiplexed imaging techniques are giving us an increasingly detailed observation of a biological system. However, …
Cite Project DOI Preprint Samui Browser Code
Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments
spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
Background. Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene …
Preprint PDF Cite Code Project Slides Source Document DOI
spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
Spatial Transcriptomics Analysis of Aβ-tau Synergy in the Inferior Temporal Cortex of the Human Brain in Alzheimer’s Disease
Poster presented at BoG2022
Project Slides
Spatial Transcriptomics Analysis of Aβ-tau Synergy in the Inferior Temporal Cortex of the Human Brain in Alzheimer’s Disease
SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor
Summary SpatialExperiment is a new data infrastructure for storing and accessing spatially resolved transcriptomics data, implemented …
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SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor
Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
We used the 10x Genomics Visium platform to define the spatial topography of gene expression in the six-layered human dorsolateral …
Preprint PDF Cite Code Dataset Project Source Document DOI
Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
Poster on the HumanPilot project for BioC2020 using spatialLIBD.
PDF Project DOI
Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex