Sample submission file for the ingestion of spatial data

The spatial transcriptomics ingestion workflow requires a sample submission file that specifies the location of the input files. The sample submission file is a tab-separated file with one row per sample. Panpipes currently supports the ingestion of Visium and Vizgen data.

The 6 columns of the sample submission file are:

sample id: Unique sample ID.

spatial_path: The root directory containing the data files. Please note, that the folder structure of the root directory needs to be structured as expected by the squidpy.read.visium (for Visium data) or squidpy.read.vizgen (for Vizgen data) functions.

spatial_filetype: Either “vizgen” or “visium”.

spatial_counts: The count matrix file. Usually filtered_feature_bc_matrix.h5 or raw_feature_bc_matrix.h5 for a Visium dataset. For Vizgen inputs, this file typically ends with _cell_by_gene.csv.

spatial_metadata: The metadata csv-file for Vizgen data. Leave empty for Visium data.

spatial_transformation: The transformation csv-file for Vizgen data. This column is optional for Vizgen data. Leave empty for Visium data.

Note, that the columns, sample_id, spatial_path, spatial_filetype, and spatial_counts are required for both, Visium and Vizgen data. The spatial_metadata(required) and spatial_transformation(optional) columns are Vizgen-specific and should be left empty for Visium data.

Example submission file

sample_id	spatial_path	spatial_filetype	spatial_counts	spatial_metadata	spatial_transformation
V1_Human_Heart	./data_visium/V1_Human_Heart	visium	V1_Human_Heart_filtered_feature_bc_matrix.h5
V1_Human_Lymph_Node	./data_visium/V1_Human_Lymph_Node	visium	V1_Human_Lymph_Node_filtered_feature_bc_matrix.h5
Mouse_Brain	./data_vizgen	vizgen	cell_by_gene_S1R1.csv	cell_metadata_S1R1.csv	images_micron_to_mosaic_pixel_transform.csv