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detectcilia

R package to detect cilia and other colored structures in confocal fluorescence microscopy images

https://github.com/sfb-elaine/detectcilia

Science Score: 52.0%

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    Organization sfb-elaine has institutional domain (www.elaine.uni-rostock.de)
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    Low similarity (10.1%) to scientific vocabulary
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Repository

R package to detect cilia and other colored structures in confocal fluorescence microscopy images

Basic Info
  • Host: GitHub
  • Owner: SFB-ELAINE
  • License: gpl-3.0
  • Language: R
  • Default Branch: master
  • Size: 17 MB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 8
Created over 7 years ago · Last pushed 9 months ago
Metadata Files
Readme License Citation

README.md

detectCilia

detectCilia is an R package to detect cilia (or other colored structures) in confocal fluorescence microscopy images.

Requirements

It is necessary to load a TIF (or a directory of TIF files) or a CZI file of either a z stack or its projection. Both the nuclei and the cilia (or other small structures) need to be labelled and captured in a specific channel.

Example code for using the R package

The following example (script) shows the capabilities of the package. The script is found in inst/testscript.R. The results of the detection will be written in the current directory (output/).

```R

Testscript for using the R package detectCilia +++++++++++++++++++++++++++

Author: Kai Budde-Sagert

Created: 2019/12/01

Last changed: 2025/06/13

Attention: This script was tested with R 4.4.1.

Delete everything in the environment

rm(list = ls())

close all open plots in RStudio

graphics.off()

Install packages

groundhog.day <- "2024-12-01" if(!any(grepl(pattern = "groundhog", x = installed.packages(), ignore.case = TRUE))){ install.packages("groundhog") }

Load packages

library(groundhog) pkgs <- c("BiocManager", "devtools", "dplyr", "magrittr", "readr", "rlang", "reticulate")

groundhog.library(pkgs, groundhog.day)

if(!("EBImage" %in% utils::installed.packages())){ print("Installing EBImage.") BiocManager::install("EBImage") }

require(EBImage)

Install Python package for reading czi files

(Users will be asked to install miniconda when starting for the first time)

if(! "czifile" %in% reticulate::pylistpackages()$package){ reticulate::py_install("czifile") }

Install the R package for reading czi images

devtools::install_github("SFB-ELAINE/readCzi@v0.4.1") require(readCzi)

Install this R package for detecting cilia in microscopy images

devtools::install_github("SFB-ELAINE/detectCilia", upgrade = "ask") require(detectCilia)

Alternatively:

devtools::load_all()

devtools::document()

devtools::check()

FIRST EXAMPLE: Find cilia in TIFs of one z-stack image ------------------

Directory of the images

input_dir <- system.file("extdata", "testImagesTif", package = "detectCilia", mustWork = TRUE)

Directory for the output

outputdirtif <- file.path(getwd(), "output")

Size of a pixel in micrometer

pixel_size <- 0.219645 # in \mu m

Distance between two layers in micrometers

slice_distance <- 0.31607# in \mu m

Manually set mask width here because image is small

nucmaskwidthheightin_pixels <- 100

Obtain all positions of cilia in every z-layer

detectCiliaoutputlist <- detectCilia::detectCilia( inputdirtif = inputdir, outputdir = outputdirtif, pixelsize = pixelsize, slicedistance = slicedistance, nucmaskwidthheightinpixels = nucmaskwidthheightinpixels, numbersizefactor = 0.2)

SECOND EXAMPLE: CZI file ------------------------------------------------

CZI FILE

Directory of the images

input_file <- system.file("extdata", "testImageCzi", "CiliaImage.czi", package = "detectCilia", mustWork = TRUE)

Directory for the output

outputdirczi <- file.path(getwd(), "output")

Obtain all positions of cilia in every z-layer

detectCiliaoutputlist2 <- detectCilia::detectCilia(inputfileczi = inputfile, outputdir = outputdirczi) ```

Owner

  • Name: SFB ELAINE - ELectrically Active ImplaNts
  • Login: SFB-ELAINE
  • Kind: organization
  • Location: Rostock, Germany

Repository of the SFB 1270 ELAINE

Citation (CITATION.cff) 

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "detectCilia" in publications use:'
type: software
license: GPL-3.0-only
title: 'detectCilia: Detect and measure the lengths of primary cilia in microscopy
  images'
version: 0.8.5
doi: 10.5281/zenodo.10521546
abstract: The package loads confocal fluorescence microscopy images and automatically
  determines the positions and lengths of primary cilia of the cells and counts nuclei.
authors:
- family-names: Budde-Sagert
  given-names: Kai
  email: kai.budde-sagert@uni-rostock.de
  orcid: https://orcid.org/0000-0001-6836-9865
preferred-citation:
  type: manual
  title: 'detectCilia: R package for detecting the lengths of primary cilia'
  authors:
  - family-names: Budde-Sagert
    given-names: Kai
    email: kai.budde-sagert@uni-rostock.de
    orcid: https://orcid.org/0000-0001-6836-9865
  year: '2024'
  notes: R package version 0.8.4
  doi: 10.5281/zenodo.10521546
  url: https://github.com/SFB-ELAINE/detectCilia
repository-code: https://github.com/SFB-ELAINE/detectCilia
url: https://github.com/SFB-ELAINE/detectCilia
contact:
- family-names: Budde-Sagert
  given-names: Kai
  email: kai.budde-sagert@uni-rostock.de
  orcid: https://orcid.org/0000-0001-6836-9865
references:
- type: article
  title: 'Studying the influence of cell culture medium composition on ciliary length
    with detectCilia: An R package for automated detection and length measurement
    of primary cilia'
  authors:
  - family-names: Budde-Sagert
    given-names: Kai
  - family-names: Krueger
    given-names: Simone
  - family-names: Sehlke
    given-names: Clemens
  - family-names: Jonitz-Heincke
    given-names: Anika
  - family-names: David
    given-names: Robert
  - family-names: Bader
    given-names: Rainer
  - family-names: Uhrmacher
    given-names: Adelinde M.
  journal: NN
  volume: '0'
  issue: '0'
  year: '2024'
  doi: NN
  start: '0'
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
  version: '>= 4.0.0'
- type: software
  title: BiocManager
  abstract: 'BiocManager: Access the Bioconductor Project Package Repository'
  notes: Imports
  url: https://bioconductor.github.io/BiocManager/
  repository: https://CRAN.R-project.org/package=BiocManager
  authors:
  - family-names: Morgan
    given-names: Martin
    email: martin.morgan@roswellpark.org
    orcid: https://orcid.org/0000-0002-5874-8148
  - family-names: Ramos
    given-names: Marcel
    email: marcel.ramos@sph.cuny.edu
    orcid: https://orcid.org/0000-0002-3242-0582
  year: '2025'
  doi: 10.32614/CRAN.package.BiocManager
  version: '>= 1.30.19'
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
  url: https://dplyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=dplyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: François
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Henry
    given-names: Lionel
  - family-names: Müller
    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2025'
  doi: 10.32614/CRAN.package.dplyr
  version: '>= 1.0.10'
- type: software
  title: EBImage
  abstract: 'EBImage: Image processing and analysis toolbox for R'
  notes: Imports
  url: https://github.com/aoles/EBImage
  repository: https://bioconductor.org/
  authors:
  - family-names: Oleś
    given-names: Andrzej
  - family-names: Pau
    given-names: Gregoire
  - family-names: Smith
    given-names: Mike
  - family-names: Sklyar
    given-names: Oleg
  - family-names: Huber
    given-names: Wolfgang
  - family-names: Barry
    given-names: with contributions from Joseph
  - family-names: Marais
    given-names: Philip A.
  year: '2025'
  doi: 10.18129/B9.bioc.EBImage
  version: '>= 4.40.0'
- type: software
  title: magrittr
  abstract: 'magrittr: A Forward-Pipe Operator for R'
  notes: Imports
  url: https://magrittr.tidyverse.org
  repository: https://CRAN.R-project.org/package=magrittr
  authors:
  - family-names: Bache
    given-names: Stefan Milton
    email: stefan@stefanbache.dk
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2025'
  doi: 10.32614/CRAN.package.magrittr
  version: '>= 2.0.3'
- type: software
  title: readCzi
  abstract: 'readCzi: readCzi: R package to read CZI image files, convert them to
    tifs, and save metadata'
  notes: Imports
  url: https://github.com/SFB-ELAINE/readCzi
  authors:
  - family-names: Budde-Sagert
    given-names: Kai
    email: kai.budde-sagert@uni-rostock.de
    orcid: https://orcid.org/0000-0001-6836-9865
  year: '2025'
  version: '>= 0.4.0'
- type: software
  title: readr
  abstract: 'readr: Read Rectangular Text Data'
  notes: Imports
  url: https://readr.tidyverse.org
  repository: https://CRAN.R-project.org/package=readr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Hester
    given-names: Jim
  - family-names: Bryan
    given-names: Jennifer
    email: jenny@posit.co
    orcid: https://orcid.org/0000-0002-6983-2759
  year: '2025'
  doi: 10.32614/CRAN.package.readr
  version: '>= 2.1.3'
- type: software
  title: rlang
  abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
  notes: Imports
  url: https://rlang.r-lib.org
  repository: https://CRAN.R-project.org/package=rlang
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.rlang
  version: '>= 1.0.6'

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