BrainStOrmics

DAG-MCTS for cell type annotation. Search space is a DAG (Merge + ReEmbed create multi-parent nodes). Uses P-UCT selection, Soft-Bellman backprop, confidence discounting, and transposition table. Per-iteration tree viz emitted as interactive HTML.

Correct batch effects in single-cell data using Harmony, BBKNN, or ComBat.

Query CellWiki knowledge base for marker genes, cell type ontologies, and tissue-specific cell type constraints.

Find differentially expressed genes (markers) for clusters using wilcoxon, t-test, or logistic regression. Includes consensus markers and resolution scanning.

Assess single-cell clustering quality using silhouette score, modularity, and phiclust. Returns recommendations to adjust resolution or accept current clustering.

Load single-cell RNA-seq data from h5ad, rds, or 10x mtx formats into AnnData objects.

Generate publication-quality UMAP/t-SNE embedding plots with Okabe-Ito color palette. Outputs PDF+PNG.

Generate violin plots and dot plots for gene expression visualization across cell clusters.

Run the complete Spateo pipeline — IO through Morphogenesis

Read spatial transcriptomics data — 10 platforms + auto-detect

Spatial alignment of tissue slices — 2D→3D registration

Vector field inference, trajectory analysis, GLM differential expression

3D model generation, gene expression interpolation, morphology analysis

Set up Spateo runtime environment — choose conda or uv

Convert research paper PDFs to Markdown with structured figure data extraction. Extracts panel-level CSV tables or descriptions from scientific figures (CNS-level papers). Use when the user wants to convert a PDF paper to MD with figure data.

运行 PDF 转 Markdown pipeline — 执行 7 步转换流程（PDF 解析、图片过滤、面板检测、描述生成、表格提取、CSV 提取、MD 组装）、质量检查、故障处理。Use when the user wants to convert a PDF paper to Markdown, run the pipeline, or check output quality.

VLM API 与工作流配置 — 配置 VLM 提供商（API key、模型、endpoint）、修改 pipeline 工作流参数、理解输入输出格式。Use when the user needs to configure API keys, change VLM models, adjust pipeline parameters, or understand the I/O contract.

环境配置 — 搭建 pdf2md 运行所需的 conda/uv 环境、安装依赖、配置 HF 中国镜像、预下载模型。Use when the user needs to set up the environment, install dependencies, fix import errors, or download models.