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数据与复现地理信息与遥感FreedomIntelligence/OpenClaw-Medical-Skills数据与复现
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spatial-transcriptomics-tutorials-with-omicverse

维护者 FreedomIntelligence · 最近更新 2026年4月1日

spatial-transcriptomics-tutorials-with-omicverse：Use this skill to navigate spatial analysis tutorials located under [`Tutorials-space`](../../omicverse_guide/docs/Tutorials-space/)。 notebooks span preprocessing utilities ([`t_crop_rotate.ipynb`](../../omicverse_guide/docs/Tutorials-space/t_crop_rotate.ipynb)，[`t_cellpose.ipynb`](../../omicverse_guide/docs/Tutorials-space/t_cellpose.ipynb))，deconvolution 框架s ([`t_decov.ipynb`](../../omicverse_guid…。

OpenClawNanoClaw分析处理复现实验spatial-tutorials🔬 omics & computational biologysingle-cell & spatial omicsguide

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/spatial-tutorials

维护者
FreedomIntelligence
许可
MIT
最近更新
2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

  • Use this skill to navigate spatial analysis tutorials located under Tutorials-space. notebooks span preprocessing utilities (t_crop_rotate.ipynb，t_cellpose.ipynb)，deconvolution 框架s (t_decov.ipynb，t_starfysh.ipynb)，、 downstream spatial modelling 或 integration tasks (t_cluster_space.ipynb，t_staligner.ipynb，t_spaceflow.ipynb，t_commot_flowsig.ipynb，t_gaston.ipynb，t_slat.ipynb，t_stt.ipynb). Follow staged instructions below to match "Preprocess"，"Deconvolution"，、 "Downstream" groupings presented in notebooks。
  • Core：omicverse，scanpy，anndata，numpy，matplotlib，squidpy (deconvolution + QC)，networkx (FlowSig graphs)。
  • 分割：cellpose，stardist，opencv-python/tifffile，optional GPU-enabled PyTorch ，用于 acceleration. t_cellpose.ipynb。
  • Deconvolution：tangram，cell2location，pytorch-lightning，pandas，h5py，plus optional GPU/CUDA stacks；Starfysh additionally needs torch，scikit-learn，、 curated signature CSVs. t_decov.ipynb，t_starfysh.ipynb。
  • Downstream modelling：scikit-learn (聚类，KMeans，ARI)，gseapy==1.0.4 ，用于 STT enrichment，commot，flowsig，torch-backed modules (STAligner，SpaceFlow，GASTON，SLAT)，plus HTML exporters (Plotly) ，用于 Sankey plots。

原始文档

SKILL.md 摘录

Preprocess

  1. Load spatial slides and manipulate coordinates
    • Import omicverse as ov, scanpy as sc, and enable plotting defaults with ov.plot_set() or ov.plot_set(font_path='Arial'). t_crop_rotate.ipynb
    • Fetch public Visium data via sc.datasets.visium_sge(...), inspect adata.obsm['spatial'], and respect uns['spatial'][library_id]['scalefactors'] when rescaling coordinates for high-resolution overlays.
    • Apply region selection and alignment helpers: ov.space.crop_space_visium(...) for bounding-box crops, ov.space.rotate_space_visium(...) followed by ov.space.map_spatial_auto(..., method='phase'), and refine offsets with ov.space.map_spatial_manual(...) before plotting using sc.pl.embedding(..., basis='spatial').
  2. Segment Visium HD tiles into cells
    • Organise Visium HD outputs (binned parquet counts, .btf histology) and load them through ov.space.read_visium_10x(path, source_image_path=...). t_cellpose.ipynb
    • Filter sparse bins (ov.pp.filter_genes(..., min_cells=3) and ov.pp.filter_cells(..., min_counts=1)) prior to segmentation.
    • Run nucleus/cell segmentation variants: ov.space.visium_10x_hd_cellpose_he(...) for H&E, ov.space.visium_10x_hd_cellpose_expand(...) to grow labels across neighbouring bins, and ov.space.visium_10x_hd_cellpose_gex(...) for gene-expression driven seeds. Harmonise labels with ov.space.salvage_secondary_labels(...) and aggregate to cell-level AnnData using ov.space.bin2cell(..., labels_key='labels_joint').
  3. Initial QC for downstream tasks
    • For Visium/DLPFC re-analyses, compute QC metrics (sc.pp.calculate_qc_metrics(adata, inplace=True)) and persist intermediate AnnData snapshots (adata.write('data/cluster_svg.h5ad', compression='gzip')) for reuse across tutorials. t_cluster_space.ipynb

适用场景

  • Use spatial-transcriptomics-tutorials-，支持-omicverse ，用于 GIS 、 remote-sensing workflows。
  • Apply spatial-transcriptomics-tutorials-，支持-omicverse to earth observation 、 spatial analysis tasks。

不适用场景

  • Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。

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