Digital histopathology by infrared spectroscopic imaging
R Bhargava - Annual Review of Analytical Chemistry, 2023 - annualreviews.org
Infrared (IR) spectroscopic imaging records spatially resolved molecular vibrational spectra,
enabling a comprehensive measurement of the chemical makeup and heterogeneity of …
enabling a comprehensive measurement of the chemical makeup and heterogeneity of …
Single-cell genomics meets human genetics
Single-cell genomic technologies are revealing the cellular composition, identities and
states in tissues at unprecedented resolution. They have now scaled to the point that it is …
states in tissues at unprecedented resolution. They have now scaled to the point that it is …
[HTML][HTML] Dissecting the treatment-naive ecosystem of human melanoma brain metastasis
J Biermann, JC Melms, AD Amin, Y Wang, LA Caprio… - Cell, 2022 - cell.com
Melanoma brain metastasis (MBM) frequently occurs in patients with advanced melanoma;
yet, our understanding of the underlying salient biology is rudimentary. Here, we performed …
yet, our understanding of the underlying salient biology is rudimentary. Here, we performed …
Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response
T cells mediate antigen-specific immune responses to disease through the specificity and
diversity of their clonotypic T cell receptors (TCRs). Determining the spatial distributions of T …
diversity of their clonotypic T cell receptors (TCRs). Determining the spatial distributions of T …
SCS: cell segmentation for high-resolution spatial transcriptomics
Spatial transcriptomics promises to greatly improve our understanding of tissue organization
and cell–cell interactions. While most current platforms for spatial transcriptomics only offer …
and cell–cell interactions. While most current platforms for spatial transcriptomics only offer …
Benchmarking spatial clustering methods with spatially resolved transcriptomics data
Spatial clustering, which shares an analogy with single-cell clustering, has expanded the
scope of tissue physiology studies from cell-centroid to structure-centroid with spatially …
scope of tissue physiology studies from cell-centroid to structure-centroid with spatially …
Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope
The rapid emergence of spatial transcriptomics (ST) technologies is revolutionizing our
understanding of tissue spatial architecture and biology. Although current ST methods …
understanding of tissue spatial architecture and biology. Although current ST methods …
Integrating spatial transcriptomics data across different conditions, technologies and developmental stages
With the rapid generation of spatial transcriptomics (ST) data, integrative analysis of multiple
ST datasets from different conditions, technologies and developmental stages is becoming …
ST datasets from different conditions, technologies and developmental stages is becoming …
Streamlining spatial omics data analysis with Pysodb
Advances in spatial omics technologies have improved the understanding of cellular
organization in tissues, leading to the generation of complex and heterogeneous data and …
organization in tissues, leading to the generation of complex and heterogeneous data and …
STAMarker: determining spatial domain-specific variable genes with saliency maps in deep learning
Spatial transcriptomics characterizes gene expression profiles while retaining the
information of the spatial context, providing an unprecedented opportunity to understand …
information of the spatial context, providing an unprecedented opportunity to understand …