ijtiff v2.0.2

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Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files

General purpose TIFF file I/O for R users. Currently the only such package with read and write support for TIFF files with floating point (real-numbered) pixels, and the only package that can correctly import TIFF files that were saved from 'ImageJ' and write TIFF files than can be correctly read by 'ImageJ' <https://imagej.nih.gov/ij/>. Also supports text image I/O.

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ijtiff

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Introduction

This is a general purpose TIFF I/O utility for R. The tiff package already exists for this purpose but ijtiff adds some functionality and overcomes some bugs therein.

  • ijtiff can write TIFF files whose pixel values are real (floating-point) numbers; tiff cannot.
  • ijtiff can read and write text images; tiff cannot.
  • tiff struggles to interpret channel information and gives cryptic errors when reading TIFF files written by the ImageJ software; ijtiff works smoothly with these images.

To learn about ijtiff and how to use it, visit the package website at https://ropensci.github.io/ijtiff.

Installation

libtiff

ijtiff requires you to have the libtiff C library installed. To install libtiff:

  • On Debian Linux, try sudo apt-get install libtiff5-dev, or if that fails, try
    sudo apt-get install libtiff4-dev.
  • On Fedora Linux, try sudo yum install libtiff5-dev, or if that doesn’t work, try
    sudo yum install libtiff4-dev.
  • On Mac, you need Homebrew. Then in the terminal, run brew install libtiff.
  • On 64-bit Windows, no setup is required

Functions in ijtiff

Name Description
write_tif Write images in TIFF format
count_frames Count the number of frames in a TIFF file.
linescan-conversion Rejig linescan images.
ijtiff ijtiff: TIFF I/O for ImageJ users
ijtiff_img ijtiff_img class.
display Basic image display.
text-image-io Read/write an image array to/from disk as text file(s).
tif_tags_reference TIFF tag reference.
read_tif Read an image stored in the TIFF format
read_tags Read TIFF tag information without actually reading the image array.
as_EBImage Convert an ijtiff_img to an EBImage::Image.
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Vignettes of ijtiff

Name
reading-and-writing-images.Rmd
text-images.Rmd
the-imagej-problem.Rmd
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