Tutorials and technical notes.

Resources A LaTeX Template for OmicVerse Papers pdarticle gives OmicVerse papers and preprints one shared look: single- or two-column layouts, four page designs, brand colors, line numbers and Chinese support. Download the ZIP and start from template.tex. Spatial Analyzing NanoString CosMx Data Read CosMx data, validate FOV-level spatial structure, inspect segmentation quality, and prepare inputs for downstream spatial modeling. Spatial Analyzing Visium HD Data Work with Visium HD bin-level output, tissue images, spatially variable genes, low-dimensional representations, and segmentation-derived views. 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. 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. 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. 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. 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. Release 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. 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.