paper/paper.md

In ropensci/ijtiff: Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files

title: 'ijtiff: An R package providing TIFF I/O for ImageJ users' tags: - R - file - string authors: - name: Rory Nolan orcid: 0000-0002-5239-4043 affiliation: 1 - name: Sergi Padilla-Parra orcid: 0000-0002-8010-9481 affiliation: 1, 2 affiliations: - name: Wellcome Centre Human Genetics, University of Oxford index: 1 - name: Department of Structural Biology, University of Oxford index: 2 date: 26 February 2018 bibliography: paper.bib nocite: | @R, @RStudio, @checkmate, @magrittr, @filesstrings, @stringr, @readr, @purrr, @Rcpp, @fields, @grDevices, @knitr, @testthat, @rmarkdown, @covr, @devtools, @exampletestr, @BioFormats, @libtiff

Summary

ImageJ [@ImageJ] is the image viewing and processing GUI of choice for many in the fields of biology and microscopy. It is free and open-source. ijtiff is an R package which can correctly import TIFF files that were saved from ImageJ and write TIFF files than can be correctly read by ImageJ. Due to the sometimes strange way that ImageJ writes TIFF files, the original R tiff package [@tiff] may not correctly recognise their channel structure. ijtiff also goes beyond tiff in facilitating the writing of floating point (real-numbered) TIFF files from R.

ijtiff reads TIFF pixel values in their native (usually integer) form, whereas tiff scales pixel values to the range [0, 1] by default. Hence and for other reasons, ijtiff should be viewed as a package with different capabilities and behaviours from the original tiff package, and not as an extension thereof.

TIFF files are not always enough: they have maximum allowed values and their 32-bit floating point real-number representation can lack precision. For these extreme cases, ijtiff also supports text image I/O. Text images have no such limitations and are completely compatible with ImageJ.

References

ropensci/ijtiff documentation built on Jan. 17, 2024, 2:19 p.m.