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, Vizgen, and Xenium data. The data of different technologies needs to be ingested separately with different sample submission files.
The minimum required (non-optional) columns for each 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 spatialdata_io.visium (for Visium data), spatialdata_io.merscope (for Vizgen data), or spatialdata_io.xenium (for Xenium data) functions.
spatial_filetype: Either “vizgen”, “visium”, or “xenium”.
Visium
The 7 columns of the Visium sample submission file are:
sample_id |
spatial_path |
spatial_filetype |
visium_feature_bc_matrix |
visium_fullres_image_file |
visium_tissue_positions_file |
visium_scalefactors_file |
|---|
The following 4 columns are optional:
visium_feature_bc_matrix: Name of the counts file. Corresponds to the counts_file parameter of spatialdata_io.visium
visium_fullres_image_file: Path to the full-resolution image. Corresponds to the fullres_image_file parameter of spatialdata_io.visium
visium_tissue_positions_file: Path to the tissue positions file. Corresponds to the tissue_positions_file parameter of spatialdata_io.visium
visium_scalefactors_file: Path to the scalefactors file. Corresponds to the scalefactors_file parameter of spatialdata_io.visium
Example submission file
Vizgen
The 6 columns of the Vizgen sample submission file are:
sample_id |
spatial_path |
spatial_filetype |
vpt_cell_by_gene |
vpt_cell_metadata |
vpt_cell_boundaries |
|---|
The following 3 columns are optional:
vpt_cell_by_gene: The file name of the output of the vizgen-postprocessing-tool. See spatialdata_io.merscope
vpt_cell_metadata: The file name of the output of the vizgen-postprocessing-tool. See spatialdata_io.merscope
vpt_cell_boundaries: The file name of the output of the vizgen-postprocessing-tool. See spatialdata_io.merscope
Example submission files MERFISH MERSCOPE
Xenium
The 3 columns of the Xenium sample submission file are:
sample_id |
spatial_path |
spatial_filetype |
|---|