A Mapping is the link between a cell segmentation and the quantitative data associated with each segmented cell. Once an Intensity Map job has completed, ariadne.ai SPATIAL creates a Mapping that stores, for every cell, the measured intensity of each marker channel. These per-cell measurements are called Properties.
Mappings are the starting point for all downstream statistical analysis in SPATIAL. The jobs t-SNE, UMAP, Automatic Cell Type Detection, Neighborhood Enrichment, Recurrent Cellular Neighborhoods, and Plotting all draw their per-cell data from a Mapping.
Think of a Mapping as a table where each row is a cell and each column is a marker or morphometric feature. SPATIAL stores this table internally and gives you access to it through the right panel and through the download function.
A Property is a single quantitative measurement assigned to every cell in a segmentation. Properties come in two kinds:
A continuous value per cell — such as the mean fluorescence intensity of a marker within the cell boundary, a morphometric measurement (e.g. area, perimeter, roundness), or a transcript count. SPATIAL stores numerical properties in a normalized form internally but always displays and exports them in their original physical units.
A discrete label assigned to each cell, such as a tissue region type (e.g. "Blood Vessel", "Tumor", "Stroma") or a cell type label produced by Automatic Cell Type Detection. Categorical properties are always shown alongside their human-readable category names and can be used as grouping variables in downstream analysis.
A single Mapping can contain any number of Properties of both kinds.
Mappings are created automatically by SPATIAL after a successful Intensity Map job. You do not need to create or configure a Mapping manually. When the job finishes, SPATIAL links the resulting per-cell measurements to the segmentation layer you selected as the target and makes them available in the right panel.
If you run additional jobs that add new measurements — for example, an Add Mapping Property job — those new Properties are appended to the existing Mapping automatically.
Each Mapping is identified by the name of the segmentation it is linked to. If your dataset contains multiple segmentations (for example, a nuclear segmentation and a whole-cell segmentation), each will have its own Mapping.
Once a Mapping is selected in the right panel, you can:
When a Mapping contains Categorical Properties, they appear as a separate section in the marker list. You can use a Categorical Property to:
You can export the full per-cell data table of any Mapping as a CSV file. This file contains one row per cell and one column per Property, with all values in their original physical units.
To download a Mapping:
dataset_[ID]_[MappingName]_markers.csvThe CSV contains:
This file can be opened directly in Excel, R, Python (pandas), or any other analysis tool for further downstream analysis outside SPATIAL.
In addition to the Properties created automatically by the Intensity Map job, you can add new computed Properties to an existing Mapping using the Add Mapping Property job. This is useful when, for example, you want to include the expression of a marker from a later staining cycle in an existing per-cell table, or when you want to add a neighborhood-based spatial feature.
This job can compute:
To submit an Add Mapping Property job, click NEW JOB and select Add Mapping Property. Select the existing Mapping to extend, the marker layers and/or segmentation layers to include, the radius and summary statistic for marker sampling, and submit. When the job completes, the new Properties will appear automatically in the selected Mapping.