https://anthbapt.github.io/tags/spatial-omics/Spatial OmicsHugoBlox Kit (https://hugoblox.com)en-usSun, 01 Sep 2024 00:00:00 +0000https://anthbapt.github.io/media/icon_hu_da05098ef60dc2e7.pnghttps://anthbapt.github.io/tags/spatial-omics/https://anthbapt.github.io/projects/mosaik/Sun, 01 Sep 2024 00:00:00 +0000https://anthbapt.github.io/projects/mosaik/<p>MOSAIK enables cross-platform integration of spatial transcriptomics data from Xenium (10x Genomics), CosMx (NanoString), and MERFISH (Vizgen) into a common SpatialData framework.</p> <p>The toolkit standardises coordinate systems, gene panels, and metadata to enable fair comparison and joint analysis across platforms.</p>https://anthbapt.github.io/courses/spatial-transcriptomics/Sun, 01 Sep 2024 00:00:00 +0000https://anthbapt.github.io/courses/spatial-transcriptomics/<p>Course materials and tutorials covering:</p> <ul> <li>Introduction to spatial transcriptomics technologies (Xenium, CosMx, MERFISH)</li> <li>Data loading and quality control with SpatialData</li> <li>Cell type annotation with CellTypist</li> <li>Spatial statistics and neighbourhood analysis</li> <li>Visualisation and interpretation</li> </ul> <p><em>Materials coming soon.</em></p>https://anthbapt.github.io/projects/metabric-mx/Sat, 01 Jun 2024 00:00:00 +0000https://anthbapt.github.io/projects/metabric-mx/<p>METABRIC-MX (Multimodal eXplorer) is a platform for processing and analysing Xenium breast cancer spatial transcriptomics data from the METABRIC cohort. The pipeline handles:</p> <ul> <li><strong>Multi-modal registration</strong>: Aligning metallomics, immunofluorescence, H&amp;E, and Xenium data into unified SpatialData/Zarr objects</li> <li><strong>Cell typing</strong>: Automated annotation using CellTypist with the Chen.pkl model trained on 600k+ cells</li> <li><strong>Batch correction</strong>: Harmony and scVI integration across tissue microarray cores</li> <li><strong>Spatial analysis</strong>: KNN smoothing, neighbourhood composition, and immune niche profiling</li> </ul>