Spatial Transcriptiomics

Visium counts file: sptrnaseq_count_table

• Objective of the file: Raw counts, log-normalized

• Example format: sptrnaseq_count_table.parquet

• Requirements:

• Named sptrnaseq_count_table

• In parquet format

• spot_id, gene_name as primary key

• Contains the mandatory columns in the table below

• File columns & description:

Name	Type	Mandatory	Description
spot_id	str	TRUE	Cell identifier
gene_name	str	TRUE	Gene name fitting HGNC ontology
count	pl.Float32	TRUE	Raw count value
count_lognorm	pl.Float32	TRUE	Log-normalized count value

Visium metadata file: sptrnaseq_metadata_table

• Objective of the file: contains spatial coordinates & cell types

• Example format: sptrnaseq_metadata_table.parquet

• Requirements:

• Named sptrnaseq_metadata_table

• In parquet format

• spot_id as primary key

• Contains the mandatory columns in the table below

• File columns & description:

Name	Type	Mandatory	Description
spot_id	str	TRUE	Spatial spot identifier
patient_id	str	TRUE	Patient identifier
spatial_1	pl.Float32	TRUE	First spatial coordinate
spatial_2	pl.Float32	TRUE	Second spatial coordinate

Other recommended columns:

'sample_id',
'hires_image_path',
'in_tissue',
'array_row',
'array_col',
'X_pca_1',
'X_pca_2',
'DominantCellType_cohort_level_2',
'Malignant_deconv_cohort_level_2_frac',
'B_cell_deconv_cohort_level_2_frac',
'DC_deconv_cohort_level_2_frac',
'Endothelial_deconv_cohort_level_2_frac',
'Epithelial_deconv_cohort_level_2_frac',
'Fibroblast_deconv_cohort_level_2_frac',
'Granulocyte_deconv_cohort_level_2_frac',
'Mast_deconv_cohort_level_2_frac',
'MoMac_deconv_cohort_level_2_frac',
'Muscle_deconv_cohort_level_2_frac',
'Neuron_deconv_cohort_level_2_frac',
'Oligodendrocyte_deconv_cohort_level_2_frac',
'Plasma_deconv_cohort_level_2_frac',
'T_NK_deconv_cohort_level_2_frac',
'Other_deconv_cohort_level_2_frac',
'fiducial_diameter_fullres',
'regist_target_img_scalef',
'spot_diameter_fullres',
'tissue_hires_scalef'

Visium sample level file: sptrnaseq_sample_level_table

• Objective of the file: region-specific metrics

• Example format: sptrnaseq_sample_level_table.parquet

• Requirements:

• Named sptrnaseq_sample_level_table

• In parquet format

• sample_id, region, gene_name as primary key

• Contains the mandatory columns in the table below

• File columns & description:

Name	Type	Mandatory	Description
sample_id		FALSE
region		FALSE
gene_name		FALSE
percentage_expressing		FALSE
avg_log_normalized_expression_expressing		FALSE
avg_log_normalized_expression_all		FALSE
total_spots		FALSE