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Human and animal tissues consist of heterogeneous cell types that organize and interact in highly structured manners. Bulk and single-cell sequencing technologies remove cells from their original microenvironments, resulting in a loss of…
Spatial transcriptomics is a modern sequencing technology that allows the measurement of the activity of thousands of genes in a tissue sample and map where the activity is occurring. This technology has enabled the study of the so-called…
The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and…
Spatial transcriptomics methods capture cellular measurements such as gene expression and cell types at specific locations in a cell, helping provide a localized picture of tissue health. Traditional visualization techniques superimpose the…
Spatial Transcriptomics is a novel technology that aligns histology images with spatially resolved gene expression profiles. Although groundbreaking, it struggles with gene capture yielding high corruption in acquired data. Given potential…
Background: Spatial transcriptomics have emerged as a powerful tool in biomedical research because of its ability to capture both the spatial contexts and abundance of the complete RNA transcript profile in organs of interest. However,…
Advances in spatially-resolved transcriptomics (SRT) technologies have propelled the development of new computational analysis methods to unlock biological insights. As the cost of generating these data decreases, these technologies provide…
Spatial Transcriptomics is a groundbreaking technology that integrates histology images with spatially resolved gene expression profiles. Among the various Spatial Transcriptomics techniques available, Visium has emerged as the most widely…
Spatial Transcriptomics (ST) profiles thousands of gene expression values at discrete spots with precise coordinates on tissue sections, preserving spatial context essential for clinical and pathological studies. With rising sequencing…
Spatial transcriptomics measures the expression of thousands of genes in a tissue sample while preserving its spatial structure. This class of technologies has enabled the investigation of the spatial variation of gene expressions and their…
The technology to generate Spatially Resolved Transcriptomics (SRT) data is rapidly being improved and applied to investigate a variety of biological tissues. The ability to interrogate how spatially localised gene expression can lend new…
Spatial transcriptomics (ST) enables transcriptome-wide profiling while preserving the spatial context of tissues, offering unprecedented opportunities to study tissue organization and cell-cell interactions in situ. Despite recent…
Spatial transcriptomics enables simultaneous measurement of gene expression and tissue morphology, offering unprecedented insights into cellular organization and disease mechanisms. However, the field lacks comprehensive benchmarks for…
In order to understand the complexities of cellular biology, researchers are interested in two important metrics: the genetic expression information of cells and their spatial coordinates within a tissue sample. However, state-of-the art…
Spatial transcriptomics assays are rapidly increasing in scale and complexity, making computational analysis a major bottleneck in biological discovery. Although frontier AI agents have improved dramatically at software engineering and…
Spatial transcriptomics is a technology that captures gene expression levels at different spatial locations, widely used in tumor microenvironment analysis and molecular profiling of histopathology, providing valuable insights into…
Spatial transcriptomics (ST) profiles gene expression across a tissue section while preserving the spatial coordinates. Because current ST technologies typically profile two-dimensional tissue slices, integrating and aligning slices from…
The spatial location of cells within tissues and organs is crucial for the manifestation of their specific functions.Spatial transcriptomics technology enables comprehensive measurement of the gene expression patterns in tissues while…
The integration of spatial multi-omics data from single tissues is crucial for advancing biological research. However, a significant data imbalance impedes progress: while spatial transcriptomics data is relatively abundant, spatial…
Spatial reasoning, which requires ability to perceive and manipulate spatial relationships in the 3D world, is a fundamental aspect of human intelligence, yet remains a persistent challenge for Multimodal large language models (MLLMs).…