R Observatory: Metrics for bioimagetools version 1.1.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bioimagetools

1.1.9

Tools for Microscopy Imaging

1packages depend

4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Volker SchmidFirst published 2016-10-149 releasesCRAN page ↗GitHub ↗

Tools for 3D imaging, mostly for biology/microscopy. Read and write TIFF stacks. Functions for segmentation, filtering and analyzing 3D point patterns.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("bioimagetools", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("bioimaginggroup/bioimagetools")

Development version from bioimaginggroup/bioimagetools. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-bioimagetools

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

Slowest check: 2.8 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

7

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 172 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 50%
Documented parameters: 96%
Return-value docs: 96%
References docs: 0%

Downloads

4K

CRAN downloads in the past year

Rank #9,112 · ~11/day · ~336/mo

Releases R versions

Daily download trend is not available in this view yet.

25930 days

1K90 days

4K1 year

Compare downloads with other packages →

Also on449 r2u

Repository

GitHub ↗ bioimaginggroup/bioimagetools

4Stars

0Forks

1Open issues

0Open PRs

0Releases

260Commits

5Contributors

microscopybiologyr

License GPL-2.0 · 260 commits · Last activity 2025-10-29

Stars over time

2022-10-06 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/bioimaginggroup/bioimagetools on 2026-08-23.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (7)

paralleltiffstatsgrDevicesutilsEBImage httr

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown abind fs R.rsp

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

nucim

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Volker Schmid

Author, Maintainer

Authors (1)

Volker Schmid

Author, Maintainer

Contributors (2)

Priyanka Kukreja

Contributor · added in 1.0.0

Fabian Scheipl

Contributor · added in 1.0.0

Package Timeline

9 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.1.9Latest
2025-09-29 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.1.8
2022-05-28 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.1.5
2020-05-29 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1.4
2020-01-15 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.1.3
2018-04-11 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.1.0
2017-02-18 · diff ↗

Show 4 earlier events

1.0.0
2016-12-01 · diff ↗
0.3.1
2016-10-17 · diff ↗
0.3.0
2016-10-14
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-10-14
Total releases: 9 / 10 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Download size: 799 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bioimagetools")

Format

Schmid, V., Kukreja, P., & Scheipl, F. (2025). bioimagetools: Tools for Microscopy Imaging (Version 1.1.9) [Computer software]. https://doi.org/10.32614/CRAN.package.bioimagetools

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for bioimagetools version 1.1.9 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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