Update single cell preprocessing notebook to current best practices

- [ ] Update scanpy version
- [ ] Update according to sc-best-practices.org
- [ ] Substitute umap figure in multiqc report from plaotpca.py to preprocess notebook result

Locate the single-cell preprocessing notebook and the multiqc report reference to plaotpca.py. Review the notebook against the current scanpy version and sc-best-practices.org, then verify that the multiqc report uses the UMAP figure produced by the preprocessing notebook. Done means all three checklist items are addressed and the report displays the updated result.

Written by the indexing model from the issue text.