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readczi

readCzi is an R package to read Carl Zeiss Image (CZI) files, convert them to tifs and store metadata

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

Science Score: 52.0%

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    Organization sfb-elaine has institutional domain (www.elaine.uni-rostock.de)
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Repository

readCzi is an R package to read Carl Zeiss Image (CZI) files, convert them to tifs and store metadata

Basic Info
  • Host: GitHub
  • Owner: SFB-ELAINE
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 66 MB
Statistics
  • Stars: 4
  • Watchers: 3
  • Forks: 1
  • Open Issues: 1
  • Releases: 6
Created about 5 years ago · Last pushed 10 months ago
Metadata Files
Readme License Citation

README.md

readCzi

readCzi is an R package to read CZI image files (images from ZEISS microscopes), stack them if needed (projection), convert the files to tifs (also normalized and histogram equalized), and store the metadata a CSV files.

Readable image/microscopy formats

The R package readCzi has been checked with image data from * ZEISS Apotome, * ZEISS AxioImager, * ZEISS laser scanning microscopes (1 to 3 channels, 1 to 3 tracks, 1 to n z layers). Please contact Kai for further information and sample data.

Example code for using the R package

The following example (script and results) shows the capabilities of the package. The script is found in inst/testscript.R.

```R

Testscript for using the R package readCzi +++++++++++++++++++++++++++++++

Author: Kai Budde-Sagert

Created: 2021/04/08

Last changed: 2024/01/17

Delete everything in the environment

rm(list = ls())

close all open plots in RStudio

graphics.off()

Load packages

groundhog.day <- "2023-01-01" if(!any(grepl(pattern = "groundhog", x = installed.packages(), ignore.case = TRUE))){ install.packages("groundhog") }

Load packages

library(groundhog) pkgs <- c("BiocManager", "devtools", "reticulate", "tibble", "xml2") groundhog.library(pkgs, groundhog.day)

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

require(EBImage)

Install Python package for reading data of 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 this R package for reading CZI images in R

if(!("readCzi" %in% installed.packages()[,"Package"])){ devtools::install_github("SFB-ELAINE/readCzi") } require(readCzi)

Please adapt the following parameters

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

Input file

inputfile <- system.file("extdata", "LSMthreeChannels.czi", package = "readCzi", mustWork = TRUE)

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

1. Read czi file and store as array -------------------------------------

imagedata <- readCzi(inputfile = input_file)

2. Read metadata of czi file and save as CSV ----------------------------

(in German and English format)

dfmetadata <- readCziMetadata(inputfile = inputfile, savemetadata = TRUE)

filepathde <- file.path(dirname(inputfile), "output", paste0(gsub("\.czi", "", basename(inputfile)), "dfmetadatade.csv")) filepathen <- file.path(dirname(inputfile), "output", paste0(gsub("\.czi", "", basename(inputfile)), "dfmetadataen.csv"))

dir.create(path = file.path(dirname(inputfile), "output"), showWarnings = FALSE) readr::writecsv(x = dfmetadata, file = filepathen) readr::writecsv2(x = dfmetadata, file = filepath_de)

3. Convert czi file to tifs ---------------------------------------------

convertCziToTif(inputfile = inputfile, convertallslices = TRUE)

```

The results are the following:

1. LSM_threeChannels.czi

  • Original images (z-stack layers + projection (maximum intensity method)):

    • Layer 1: Original converted LSM image (z-stack layer 1)
    • Layer 2: Original converted LSM image (z-stack layer 2)
    • ...
    • Layer 15: Original converted LSM image (z-stack layer 15)
    • Layer 16: Original converted LSM image (z-stack layer 16)
    • Layer 17: Original converted LSM image (z-stack layer 17)
    • Layer 18: Original converted LSM image (z-stack layer 18)
    • Layer 19: Original converted LSM image (z-stack layer 19)
    • Layer 20: Original converted LSM image (z-stack layer 20)
    • Layer 21: Original converted LSM image (z-stack layer 21)
    • Layer 22: Original converted LSM image (z-stack layer 22)
    • Layer 23: Original converted LSM image (z-stack layer 23)
    • Layer 24: Original converted LSM image (z-stack layer 24)
    • Layer 25: Original converted LSM image (z-stack layer 25)
    • Z-stack projection (maximum intensity method): Original converted LSM image (z-stack projection)
    • Histogram equalized z-stack projection (using the clahe method of the EBImage R package): Histogram equalized LSM z-stack projection
    • Normalized histogram equalized z-stack projection (normalizing each channel separately): Normalized and histogram equalized LSM z-stack projection

(The jpgs were created with the R package 'magick'. Please see ´inst/testscript.R´ for details.)

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 "readCzi" in publications use:'
type: software
license: GPL-3.0-only
title: 'readCzi: Read CZI image files, convert them to tifs, and save metadata'
version: 0.4.2
doi: 10.5281/zenodo.10231885
abstract: The package reads (z-stack) CZI microscopy files, edits them, and stores
  the results in the tif format. The metadata is also read, transformed into a tibble,
  and saved as a CSV file.
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: 'readCzi: R package to read CZI image files, convert them to tifs, and save
    metadata'
  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 0.4.1
  doi: 10.5281/zenodo.10231885
  url: https://github.com/SFB-ELAINE/readCzi
repository-code: https://github.com/SFB-ELAINE/readCzi
url: https://github.com/SFB-ELAINE/readCzi
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: 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: 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: reticulate
  abstract: 'reticulate: Interface to ''Python'''
  notes: Imports
  url: https://rstudio.github.io/reticulate/
  repository: https://CRAN.R-project.org/package=reticulate
  authors:
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Tang
    given-names: Yuan
    email: terrytangyuan@gmail.com
    orcid: https://orcid.org/0000-0001-5243-233X
  year: '2025'
  doi: 10.32614/CRAN.package.reticulate
  version: '>= 1.26'
- type: software
  title: tibble
  abstract: 'tibble: Simple Data Frames'
  notes: Imports
  url: https://tibble.tidyverse.org/
  repository: https://CRAN.R-project.org/package=tibble
  authors:
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2025'
  doi: 10.32614/CRAN.package.tibble
  version: '>= 3.1.8'
- type: software
  title: xml2
  abstract: 'xml2: Parse XML'
  notes: Imports
  url: https://xml2.r-lib.org
  repository: https://CRAN.R-project.org/package=xml2
  authors:
  - family-names: Wickham
    given-names: Hadley
  - family-names: Hester
    given-names: Jim
  - family-names: Ooms
    given-names: Jeroen
    email: jeroenooms@gmail.com
  year: '2025'
  doi: 10.32614/CRAN.package.xml2
  version: '>= 1.3.3'

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Dependencies

DESCRIPTION cran
  • BiocManager * imports
  • EBImage * imports
  • reticulate * imports
  • xml2 * imports
.github/workflows/update-citation-cff.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite