Tutorials and technical notes from OmicVerse.

Spatial Analyzing NanoString CosMx Data Read CosMx data, validate FOV-level spatial structure, inspect segmentation quality, and prepare inputs for downstream spatial modeling. Read → Spatial Analyzing Visium HD Data Work with Visium HD bin-level output, tissue images, spatially variable genes, low-dimensional representations, and segmentation-derived views. Read → Spatial Analyzing Xenium Data Load a 10x Xenium outs folder into AnnData, keep cell polygon boundaries, run QC and Leiden clustering, then project clusters back onto tissue space. Read → Spatial Reading and Preprocessing Atera Data Use OmicVerse to read 10x Atera whole-transcriptome spatial data, align expression, centroids, boundaries, nuclei, morphology channels, and annotations. Read → Segmentation Cell Segmentation for Visium HD with Cellpose Connect Visium HD 2 um bins, H&E images, Cellpose segmentation, and bin-to-cell aggregation in a pure Python workflow. Read → Visualization Circular UMAPs with the Python Version of plot1cell Use ov.pl.plot1cell to place UMAP or t-SNE cells inside a circular layout and add cluster-aware metadata rings around the embedding. Read → Single-cell How to Choose Leiden Resolution Compare manual Leiden, bootstrap stability, and CHAMP on PBMC8k to choose a reproducible starting resolution for single-cell clustering. Read → Release What Changed in OmicVerse 2.1.x A compact English release note for the 2.1.x line: pure-Python Monocle, Xenium and Visium HD workflows, plotting updates, agent runtime work, metabolomics, and microbiome support. Read → Agents What Anthropic Mythos Preview Signals for Agent Security A security-oriented note on why increasingly capable agents need bounded execution, provenance, credential discipline, and auditable scientific workflows. Read →