Ingesting spatial data

The spatial_qc workflow ingests Vizgen, Visium, or Xenium data and saves the data into SpatialData objects. A primary difference to the cell suspension ingestion workflow is that we are not concatenating the input data into a single matrix, but keeping the samples as separate SpatialData objects. This ensures that the processing does not introduce any technical batch effect when tissue slides are very different in cell composition.

Steps

  • Data is ingested into SpatialData objects. The workflow generates one SpatialData per dataset.

    • SpatialData objects of the raw data are saved into ./tmp as zarr files

  • QC metrics are computed using scanpy functionalities:

    • Basic QC metrics are computed using sc.pp.calculate_qc_metrics

    • (Optional) Compute cell-cycle scores using sc.tl.score_genes_cell_cycle. For that, the default gene list can be used or a path to a tsv file can be specified.

    • (Optional) Custom genes actions. Default gene list can be used or a path to a csv file can be specified.

      • Calculate proportions of gene groups, e.g. mitochondrial genes

      • Score genes using sc.tl.score_genes

    • SpatialData objects with calculated QC metrics are saved in qc.data

    • Metadata (.obs) is saved into the current directory as tsv files

  • Specified QC metrics are plotted in violin and spatial embedding plots

    • For Vizgen data, additional histograms are plotted

Steps to run

  1. Generate sample submission file. You can find more information about the generation here

  2. (Optional) Generate QC gene lists as described in gene list format

  3. Activate conda environment conda activate pipeline_env

  4. Generate yaml and log file panpipes qc_spatial config

  5. Specify the parameter setting in the pipeline.yml file

  6. Run complete QC workflow with panpipes qc_spatial make full --local

  7. Use outputs to decide filtering thresholds

    • Note that the actual filtering occurs in the first step of the preprocess_spatial workflow

The Ingesting 10X Visium data with Panpipes and Ingesting MERFISH data with Panpipes tutorials guide you through the ingestion step by step.