omicverse-single-cell-cytotrace2

OmicVerse Single-Cell CytoTRACE2

Goal

Run the reusable CytoTRACE2 execution spine on single-cell AnnData: prepare the expression matrix, ensure pretrained weights are available, run ov.single.cytotrace2(...), capture the score and potency columns written into adata.obs, and optionally overlay those outputs on an existing embedding. Keep the skill centered on the potency-prediction job rather than on the tutorial dataset.

Quick Workflow

1. Inspect the input AnnData, especially whether adata.X contains the expression values you want CytoTRACE2 to score and whether the gene symbols match the declared species.
2. If the object still needs notebook-style normalization and HVG annotation, run ov.pp.preprocess(...) first and choose the mode branch explicitly.
3. Ensure the pretrained CytoTRACE2 weight directory is present before inference; download or stage it if needed.
4. Run ov.single.cytotrace2(...) with explicit species, batch settings, and parallelization settings.
5. Treat the returned table plus the five adata.obs columns as the shared handoff point for optional visualization.
6. Only if the user asks for plots, overlay CytoTRACE2_Score, CytoTRACE2_Potency, or CytoTRACE2_Relative on an existing embedding.
7. Validate the expected output columns and result table before treating the run as complete.

Interface Summary

• ov.pp.preprocess(adata, mode='shiftlog|pearson', target_sum=500000.0, n_HVGs=2000, organism='human', no_cc=False, batch_key=None, identify_robust=True) adds a counts layer, robust-gene filtering, and HVG annotations.
• mode is a two-stage branch string split on |: the first token controls normalization (shiftlog or pearson), and the second controls HVG selection (pearson or seurat).
• ov.single.cytotrace2(adata, use_model_dir, species='mouse', batch_size=10000, smooth_batch_size=1000, disable_parallelization=False, max_cores=None, max_pcs=200, seed=14, output_dir='cytotrace2_results') runs pretrained CytoTRACE2 scoring on adata.X.
• species is a real branch with at least mouse and human; the implementation warns when the casing of gene symbols looks inconsistent with the declared species.
• disable_parallelization and max_cores control worker selection through calculate_cores_to_use(...).
• batch_size controls chunking of the prediction stage; smooth_batch_size controls chunking of the KNN smoothing stage.
• Successful CytoTRACE2 runs write CytoTRACE2_Score, CytoTRACE2_Potency, CytoTRACE2_Relative, preKNN_CytoTRACE2_Score, and preKNN_CytoTRACE2_Potency into adata.obs, and also return a result table with those columns.
• The notebook uses ov.utils.embedding(...) for plotting; in current OmicVerse that is a compatibility wrapper, so treat embedding overlay as optional presentation rather than as part of the core potency job.

Boundary

• Keep this as one skill because the notebook contains one tight job: optional preprocessing, CytoTRACE2 inference, then immediate inspection of the resulting potency columns.
• Do not split the embedding overlay into a separate skill unless the user already has CytoTRACE2 outputs and wants only a plotting helper.
• Do not absorb unrelated trajectory inference, annotation, or general preprocessing notebooks here.
• If a future notebook only changes species, batch sizes, or preprocessing mode, update this skill instead of creating a duplicate.

Branch Selection

• Use mode='shiftlog|pearson' for the notebook path when you want log-normalization followed by Pearson-residual HVG selection.
• Use a first-token pearson normalization branch only when you explicitly want Pearson-residual normalization instead of shifted log normalization.
• Use a second-token seurat HVG branch only when you intentionally want Seurat-v3 HVG selection instead of Pearson-residual HVGs.
• Use species='mouse' for mixed-case mouse-style gene symbols and species='human' for mostly uppercase human-style symbols.
• Keep disable_parallelization=False for large runs when CPU parallelism is acceptable; set it to True for a simpler portable path or bounded smoke checks.
• Leave max_cores=None when automatic worker selection is acceptable; set it explicitly only when you need to cap concurrency.
• Keep batch_size at or below the dataset size; values above the cell count are reset internally.
• Avoid tiny datasets for production use. Current OmicVerse CytoTRACE2 fails on the branch where a chunk has fewer than 100 cells, because the skipped smoothing path does not produce the later CytoTRACE2_Score column expected by the wrapper.

Input Contract

• Start from an AnnData whose adata.X is the matrix you want CytoTRACE2 to score.
• Ensure gene symbols are appropriate for the declared species.
• Keep an embedding such as X_umap only if you need the optional visualization stage; CytoTRACE2 itself does not require it.
• Ensure pretrained model weights are staged before the inference call.
• Expect intermediate files and a final tab-delimited result table to be written under the requested output directory.

Minimal Execution Patterns

import omicverse as ov

adata = ov.pp.preprocess(
    adata,
    mode="shiftlog|pearson",
    n_HVGs=2000,
)

results = ov.single.cytotrace2(
    adata,
    use_model_dir=model_dir,
    species="mouse",
    batch_size=10000,
    smooth_batch_size=1000,
    disable_parallelization=False,
    output_dir="cytotrace2_results",
)

# Bounded smoke-style path
results = ov.single.cytotrace2(
    adata,
    use_model_dir=model_dir,
    species="mouse",
    batch_size=120,
    smooth_batch_size=60,
    disable_parallelization=True,
    max_pcs=50,
    output_dir="cytotrace2_smoke",
)

# Optional embedding overlays after a successful run
ov.utils.embedding(
    adata,
    basis="X_umap",
    color=["CytoTRACE2_Score", "CytoTRACE2_Potency"],
    frameon="small",
)

Validation

• Check that the model-weight directory exists before calling ov.single.cytotrace2(...).
• Check that the returned table contains CytoTRACE2_Score, CytoTRACE2_Potency, CytoTRACE2_Relative, preKNN_CytoTRACE2_Score, and preKNN_CytoTRACE2_Potency.
• Check that those same five fields were written into adata.obs.
• Check that the output directory contains the final result table after the run.
• If you used a bounded smoke path, keep at least 100 cells so the current implementation reaches the working smoothing branch.
• If the declared species disagrees with the observed gene-symbol casing warnings, stop and correct the species assumption instead of trusting the scores.
• If you only validated the bounded CPU smoke path, say so explicitly and do not claim a full large-scale reproduction.

Resource Map

• Read the branch-selection reference when choosing preprocessing mode, species, or concurrency settings.
• Read the source-grounding reference before extending the skill with more interface-specific claims.
• Read the notebook-map reference when deciding whether a future CytoTRACE2 tutorial belongs here or should become a separate downstream-only plotting skill.
• Read the compatibility reference when a run is small, parallelization behavior matters, or the wrapper fails on an edge case.