simpleSeg
Bioc currentA package to perform simple cell segmentation
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained from multiple images.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
18 2 exported
Complexity
5.5 avg / 36 max
Call network
18 nodes / 15 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
1,636
Files
100
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
2
Internal functions
16
Testing
Has tests
Yes
Test-to-code ratio
0.09
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2023-01-27
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 3
- Examples that run
- 100%2 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
2 development-tooling and community-health practices detected across 1 family in the upstream repository
Checks run against github.com/sydneybiox/simpleseg on 2026-10-21.
Topics
Depended on by (2)
Suggested by (1)
People
- Ellis Patrick author maintainer
- Nicolas Canete author
- Alexander Nicholls author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("simpleSeg")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.