SPIAT
Bioc currentSpatial Image Analysis of Tissues
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
61 52 exported
Complexity
6 avg / 30 max
Call network
61 nodes / 51 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
9,888
Files
149
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
52
Internal functions
9
Testing
Has tests
Yes
Test-to-code ratio
0.15
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
50%
Unsafe pattern score
6
Dep constraint coverage
50%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2.0
System requirements
–
C++ standard
–
License
Artistic-2.0 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2022-12-20
Latest release
2026-04-28
Avg cadence
195 days
Cold removal rate
–
Dep drift
7
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 56 (1 internal)includes a package overview page
- Examples that run
- 100%52 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Basic analyses with SPIAT HTML
- Quantifying cell colocalisation with SPIAT HTML
- Reading in data and data formatting in SPIAT HTML
- Identifying cellular neighborhood with SPIAT HTML
- Quality control and visualisation with SPIAT HTML
- Spatial heterogeneity with SPIAT HTML
- Overview of the SPIAT package HTML
- Characterising tissue structure with SPIAT HTML
Repository practices
4 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/trigosteam/spiat on 2026-10-22.
GitHub Pages site last deployed 2026-01-31 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| defined_image | – | – | – |
| image_no_markers | – | – | – |
| simulated_image | – | – | – |
| tiny_cellprofiler | data.frame | 9 × 13 | No other package |
| tiny_codex | data.frame | 9 × 14 | No other package |
| tiny_codex_phenotypes | data.frame | 37 × 2 | No other package |
| tiny_halo | data.frame | 10 × 71 | No other package |
| tiny_inform | – | – | – |
Topics
People
- Yuzhou Feng author maintainer
- Maria Doyle author
- Mabel Li author
- Volkan Ozcoban author
- Anna Trigos author
- Tianpei Yang author
- John Zhu author
Cite
Cite this package
Run in R for the authors' entry:
citation("SPIAT")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/s41467-023-37822-0.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.