The Atlas page provides a full-cell interactive view of scMaizeAtlas for exploring embeddings, annotations, sample origins, regional composition, and gene expression patterns.

• Loading: a static preview is shown first, then the full interactive atlas is enabled after coordinates and annotations finish loading.
• Embedding: switch between available layouts such as UMAP and T-SNE.
• Color points by: color cells by annotation layers including cell type, major cell type, tissue, project, variety, platform, stage, genotype, or batch.
• Gene expression: type a gene symbol or stable ID for fuzzy search, use arrow keys to choose a matched gene, press Enter or Apply, and use Reset to return to annotation coloring.
• Expression scale: when a gene is applied, the color scale indicates not detected, low expression, and high expression; point tooltips report the selected gene value for each cell.
• Filters and statistics: narrow the view by tissue, cell type, or project; the Filtered cells panel summarizes the current cell count, percentage, and top annotation composition.
• Navigation: scroll to zoom, drag to pan, hover over points for cell metadata, and use reset buttons to return to the full atlas view.
• Region selection: hold Shift and drag on the plot to select a region; the Selection panel reports the selected cells and their main tissue, cell type, and project composition.
• Export: use Download PNG to save the current Atlas view, including the active embedding, filters, zoom, and gene-expression coloring.

Typical workflow: choose UMAP or T-SNE, filter to a tissue or cell type, query a marker gene, inspect expression and tooltips, then Shift-drag a region or download the current view for reporting.