Index

01-In-situ-spatial-output

Primary analysis

Spatial in-situ imaging-based systems provide an output directory for each processed slides. Default systems parameters should provide data of suffisant quality,but possibilities exists to improve the quality of this primary analysis, prior to run statistical analysis modules. It will mainly depends on the in-situ imaging-based systems used.

Module specifications

Input data	Computational environnement	Output data
	Raw_sequencing_data_processing Bash	Spatial positions

Code

Vizgen Mercsope

ls -lh 000-DATA-vizgen/slide1/region_R0/
cell_boundaries.parquet # cell polygons
cell_by_gene.csv # expression matrix
cell_metadata.csv # cell metadata
detected_transcripts.csv # detected transcripts (x,y,z) positions
summary.png # QC of slide1 experiment
images/
    manifest.json
    micron_to_mosaic_pixel_transform.csv # micron to mosaic (tif) conversion matrix trasnformation
    mosaic_DAPI_z2.tif # DAPI z=2 tif files

In case you want to reprocess the data, vizgen provide the Vizgen Post-processing Tool (VPT) enabling users to reprocess and refine the single-cell results of MERSCOPE experiments. VPT is a command line tool that emphasizes scalable, reproducible analysis, and can be run on a workstation, a cluster, or be deployed in a cloud computing environment.

10x Genomics Xenium

ls -lh 000-DATA-xenium/output-XETG00350__0029008_slide1/
#analysis/
analysis_summary.html # QC of slide1 experiment
analysis.zarr.zip
#aux_outputs/
#cell_boundaries.csv.gz
cell_boundaries.parquet # cells polygons
#cell_feature_matrix
#cell_feature_matrix.h5
cell_feature_matrix.zarr.zip # expression matrix
#cells.csv.gz
#cells.parquet
cells.zarr.zip # cell metadata
experiment.xenium # to start xenium explorer
gene_panel.json # gene panel information
metrics_summary.csv
morphology_focus
morphology.ome.tif # morphology image
nucleus_boundaries.csv.gz # nuclei polygons
nucleus_boundaries.parquet # nuclei polygons
transcripts.parquet # detected transcripts (x,y,z) positions
transcripts.zarr.zip # detected transcripts (x,y,z) positions

This directory is fully configure to be launched into the Xenium Explorer. The .zarr files will be update in the following statistical analysis modules, for instance, to include the cell type labels. In case you neeed to refine the primary analysis you may want to run the Xenium Ranger directly using this default output directory.

Nanostring cosmx

ls -lh 000-DATA-cosmx/slide1/
CellComposite/
CellLabels/
CellOverlay/
CompartmentLabels/
miniQC_table_Colon.csv
processed_metadata_Colon.csv
slide1_exprMat_file.csv # expression matrix
slide1_fov_positions_file.csv  # individual field of view positions
slide1_metadata_file.csv # cell metadata
slide1-polygons.csv # cell polygons
slide1_tx_file.csv # detected transcripts (x,y,z) positions

Depending on your favorite expertise you will choose either a R or Python framework that all enable to read those default output directories. Here is a non-exhaustive list of the workflows you can select to setup your subsequent statistical analysis:

We do recommand the SpatialData structure, part of the scverse ecosystem, based on the very popular single-cell Anndata object.