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The _ImageJ_ Problem

2024-10-26

Source: vignettes/the-imagej-problem.Rmd
the-imagej-problem.Rmd

Introduction

The ImageJ software (https://imagej.net/ij/) is a widely-used image viewing and processing software, particularly popular in microscopy and life sciences. It supports the TIFF image format (and many others). It reads TIFF files perfectly, however it can sometimes write them in a peculiar way, meaning that when other softwares try to read TIFF files written by ImageJ, mistakes can be made.

One goal of the ijtiff R package is to correctly import TIFF files that were saved from ImageJ.

Frames and Channels in TIFF files

  • In a volumetric image, frames are typically the different z-slices. In a time-stack of images (i.e. a video), each frame represents a time-point.
  • There is one channel per colour. A conventional colour image is made up of 3 colour channels: red, green and blue. A grayscale (black and white) image has just one channel. It’s possible to acquire two channels (e.g. red an blue but not green), five channels (e.g. infrared, red, green, blue and ultraviolet), or any number at all, but these cases are seen mostly in specialist imaging fields like microscopy.

The Peculiarity of ImageJ TIFF files

It is common to use TIFFTAG_SAMPLESPERPIXEL to record the number of channels in a TIFF image, however ImageJ sometimes leaves TIFFTAG_SAMPLESPERPIXEL with a value of 1 and instead encodes the number of channels in TIFFTAG_IMAGEDESCRIPTION which might look something like
"ImageJ=1.51 images=16 channels=2 slices=8".

A conventional TIFF reader would miss this channel information (because it is in an unusual place). ijtiff does not miss it. We’ll see an example below.

Note: These peculiar ImageJ-written TIFF files are still bona fide TIFF files according to the TIFF specification. They just break with common conventions of encoding channel information.

Reading ImageJ TIFF files 

path_2ch_ij <- system.file("img", "Rlogo-banana-red_green.tif",
  package = "ijtiff"
)

path_2ch_ij is the path to a TIFF file which was made in ImageJ from the R logo dancing banana GIF used in the README of Jeroen Ooms’ magick package. The TIFF is a time-stack containing only the red and green channels of the first and third frames of the original GIF. Here’s the full gif:

Here are the red and green channels of the first and third frames of the TIFF:

The original tiff package

When we import it with the original tiff package:

img <- tiff::readTIFF(path_2ch_ij, all = TRUE)
str(img) # 10 images
#> List of 4
#>  $ : num [1:155, 1:200, 1:3] 0.996 0.996 0.996 0.996 0.996 ...
#>  $ : num [1:155, 1:200, 1:3] 0 0 0 0 0 0 0 0 0 0 ...
#>  $ : num [1:155, 1:200, 1:3] 0.996 0.996 0.996 0.996 0.996 ...
#>  $ : num [1:155, 1:200, 1:3] 0 0 0 0 0 0 0 0 0 0 ...
img[[1]][100:105, 50:55, 1] # print a section of the first image in the series
#>           [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
#> [1,] 0.6601663 0.6601663 0.6523537 0.6601663 0.7031357 0.9179828
#> [2,] 0.6718853 0.6406348 0.6718853 0.6406348 0.6406348 0.6718853
#> [3,] 0.6523537 0.6601663 0.6406348 0.6601663 0.6601663 0.6406348
#> [4,] 0.6406348 0.6406348 0.6601663 0.6406348 0.6601663 0.6406348
#> [5,] 0.6718853 0.6718853 0.6406348 0.6601663 0.6406348 0.6601663
#> [6,] 0.6718853 0.6406348 0.6406348 0.6406348 0.6523537 0.6523537
  • We just get a list of 4 frames, with wrong information about the channels (it looks like there are 3 channels per frame).
  • The numbers in the image array(s) are (by default) normalized to the range [0, 1].

The ijtiff package

When we import the same image with the ijtiff package:

img <- ijtiff::read_tif(path_2ch_ij)
#> Reading Rlogo-banana-red_green.tif: an 8-bit, 155x200 pixel
#> image of unsigned integer type. Reading 2 channels and 2
#> frames . . .
#> Done.
dim(img) # 2 channels, 2 frames
#> [1] 155 200   2   2
img[100:105, 50:55, 1, 1] # print a section of the first channel, first frame
#>      [,1] [,2] [,3] [,4] [,5] [,6]
#> [1,]  169  169  167  169  180  235
#> [2,]  172  164  172  164  164  172
#> [3,]  167  169  164  169  169  164
#> [4,]  164  164  169  164  169  164
#> [5,]  172  172  164  169  164  169
#> [6,]  172  164  164  164  167  167
  • We see the image nicely represented as an array of channels of frames.
  • The numbers in the image are integers, the same as would be seen if one opened the image with ImageJ.

Note

The original tiff package reads several types of TIFFs correctly, including many that are saved from ImageJ. This is just an example of a TIFF type that it doesn’t perform so well with.

Advice for all ImageJ users

Base ImageJ (similar to the tiff R package) does not properly open some perfectly good TIFF files1 (including some TIFF files written by the tiff and ijtiff R packages). Instead it often gives you the error message: imagej can only open 8 and 16 bit/channel images. These images in fact can be opened in ImageJ using the wonderful Bio-Formats plugin.