Package: Bioi 0.2.10

Bioi: Biological Image Analysis

Single linkage clustering and connected component analyses are often performed on biological images. 'Bioi' provides a set of functions for performing these tasks. This functionality is implemented in several key functions that can extend to from 1 to many dimensions. The single linkage clustering method implemented here can be used on n-dimensional data sets, while connected component analyses are limited to 3 or fewer dimensions.

Authors:Zachary Colburn

Bioi_0.2.10.tar.gz
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Bioi_0.2.10.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Bioi/json (API)
NEWS

# Install 'Bioi' in R:

install.packages('Bioi', repos = c('https://zcolburn.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zcolburn/bioi/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

biological-data-analysis biology cell cpp image-analysis microscopy cpp

3.81 score 13 scripts 231 downloads 6 exports 21 dependencies

Last updated from:31137ab2a3. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	142
linux-devel-x86_64	OK	150
source / vignettes	OK	180
linux-release-arm64	OK	135
linux-release-x86_64	OK	139
macos-release-arm64	OK	122
macos-release-x86_64	OK	223
macos-oldrel-arm64	OK	201
macos-oldrel-x86_64	OK	225
windows-devel	OK	142
windows-release	OK	105
windows-oldrel	OK	113
wasm-release	OK	118

Exports:.perform_grouping .perform_partitioning euclidean_linker find_blobs find_min_dists identify_thresholded_objects

Dependencies:assertthat cli cpp11 dplyr generics glue igraph lattice lifecycle magrittr Matrix pillar pkgconfig R6 Rcpp rlang tibble tidyselect utf8 vctrs withr

Bioi

Zachary Colburn

Rendered fromBioi.Rmdusingknitr::rmarkdownon May 13 2026.

Last update: 2018-01-15
Started: 2017-12-31

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Return the group number for each localization.	.euclidean_linker_cpp
For all points in matrix 1, return the distance to and index of the nearest point in matrix 2.	.find_min_dists_cpp
Return the group number for each localization.	.perform_grouping
Return the group number for each localization.	.perform_partitioning
'Bioi' package	Bioi
Return the group number for each localization.	euclidean_linker
Assign all neighboring pixels the same group number.	find_blobs
For all points in matrix 1, return the distance to and index of the nearest point in matrix 2.	find_min_dists
Assign all neighboring pixels the same group number.	identify_thresholded_objects