Journal: Seminars in Immunopathology

Article Title: How will artificial intelligence and bioinformatics change our understanding of IgA Nephropathy in the next decade?

doi: 10.1007/s00281-021-00847-y

Figure Lengend Snippet: Outline of big-data methodologies and their applications in “omics” fields

Article Snippet: Spatial transcriptomics , Fluorescent microscopy probes binding to specific transcripts and barcoding methods, targeting synthesis, are used to provide positional context for expressed genes.

Techniques: Next-Generation Sequencing, Sequencing, Amplification, Gene Expression, RNA Sequencing, Microscopy, Binding Assay, Targeted Proteomics, Mass Spectrometry, Nuclear Magnetic Resonance, Spectroscopy, Functional Assay, Imaging, Staining, Construct, Mass Cytometry, Single Photon Emission Computed Tomography

Journal: bioRxiv

Article Title: An integrative spatial multi-omic workflow for unified analysis of tumor tissue

doi: 10.1101/2024.10.15.618574

Figure Lengend Snippet: A. Distribution of cell types annotated by nuclei-only and cell-morphology segmentation. Sample annotated by cell type, showing only nuclei which share the same cell type annotations with cell-morphology segmentation. B. IF tile scan conducted post 10x Genomics Xenium data acquisition, showing cells stained for glial fibrillary protein (GFAP, green), actin (Phalloidin, magenta) and nuclei (DAPI, cyan). Scale, 1 mm. Inset indicated in red box, used in C. Scale, 50 µm. C. Structural comparison between polygons generated from expansion-based segmentation (top, left), overlaid with IF (bottom, left) and nuclei-only with overlaid cell-morphology segmentation (top, right), overlaid with IF (bottom, right). Scale, 10 µm. D. Comparison of cell area between expansion-based and cell-morphology segmentation strategies, only considering cells identified by both segmentations. The x-axis is the size of cell area as estimated by cell-morphology and the y-axis is the size of cell area estimated by expansion-based segmentation. Points are colored by the average number of nearest neighbors within 15 µm between the two segmentation strategies. E. Comparison of circular ratio between expansion-based and cell-morphology segmentation strategies for matched cells identified by both segmentations. This ratio for a particular cell mask is calculated by dividing the area of the maximum inscribed circle by the area of minimum binding circle. The x-axis is the ratio based on cell-morphology segmentations, and the y-axis is the ratio based on expansion-based segmentations. Cells are colored by the average number of nearest neighbors within 15 µm between the two segmentation strategies.

Article Snippet: Here, we address these challenges and present Spatial Multi-omics Integration (SMINT), a unified analysis framework for the effective analysis of ST (10x Genomics Xenium, 339 gene custom panel) and SM (MALDI-IMS) data generated from sequential sections of surgically resected low-grade glioma.

Techniques: Staining, Comparison, Generated, Binding Assay