A hitchhiker's guide through the bio‐image analysis software universe
Modern research in the life sciences is unthinkable without computational methods for
extracting, quantifying and visualising information derived from microscopy imaging data of …
extracting, quantifying and visualising information derived from microscopy imaging data of …
[HTML][HTML] A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung
The lung contains numerous specialized cell types with distinct roles in tissue function and
integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a …
integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a …
Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin
The spatiotemporal regulation of cell fate specification in the human developing spinal cord
remains largely unknown. In this study, by performing integrated analysis of single-cell and …
remains largely unknown. In this study, by performing integrated analysis of single-cell and …
The spatial landscape of gene expression isoforms in tissue sections
K Lebrigand, J Bergenstråhle, K Thrane… - Nucleic Acids …, 2023 - academic.oup.com
In situ capturing technologies add tissue context to gene expression data, with the potential
of providing a greater understanding of complex biological systems. However, splicing …
of providing a greater understanding of complex biological systems. However, splicing …
Visualization and quality control tools for large-scale multiplex tissue analysis in TissUUmaps3
Large-scale multiplex tissue analysis aims to understand processes such as development
and tumor formation by studying the occurrence and interaction of cells in local …
and tumor formation by studying the occurrence and interaction of cells in local …
Points2Regions: Fast, interactive clustering of imaging‐based spatial transcriptomics data
Imaging‐based spatial transcriptomics techniques generate data in the form of spatial points
belonging to different mRNA classes. A crucial part of analyzing the data involves the …
belonging to different mRNA classes. A crucial part of analyzing the data involves the …
Seeded iterative clustering for histology region identification
Annotations are necessary to develop computer vision algorithms for histopathology, but
dense annotations at a high resolution are often time-consuming to make. Deep learning …
dense annotations at a high resolution are often time-consuming to make. Deep learning …
[PDF][PDF] Points2regions: Fast interactive clustering of in situ transcriptomics data
Investigation of the spatial cellular architecture in tissue is crucial for furthering our
understanding of biological processes and diseases. The location of different cell types can …
understanding of biological processes and diseases. The location of different cell types can …
Cellular and molecular heterogeneities and signatures, and pathological trajectories of fatal COVID-19 lungs defined by spatial single-cell transcriptome analysis
Despite intensive studies during the last 3 years, the pathology and underlying molecular
mechanism of coronavirus disease 2019 (COVID-19) remain poorly defined. Here, we …
mechanism of coronavirus disease 2019 (COVID-19) remain poorly defined. Here, we …
[PDF][PDF] Tissuumaps 3 tools for visualization & quality control in large-scale multiplex tissue analysis
Large-scale multiplex tissue analysis aims to understand processes such as development
and tumor formation by studying the occurrence and interaction of cells in local …
and tumor formation by studying the occurrence and interaction of cells in local …