ijtiff

Reading ImageJ TIFF files

path_2ch_ij <- system.file("img", "2ch_ij.tif", package = "ijtiff")

path_2ch_ij is the path to a 2-channel, five-frame image which was saved from ImageJ.

The original `tiff` library

When we import it with the original tiff library:

img <- tiff::readTIFF(path_2ch_ij, all = TRUE)
#> Warning in tiff::readTIFF(path_2ch_ij, all = TRUE): TIFFReadDirectory:
#> Unknown field with tag 50838 (0xc696) encountered
#> Warning in tiff::readTIFF(path_2ch_ij, all = TRUE): TIFFReadDirectory:
#> Unknown field with tag 50839 (0xc697) encountered
str(img)  # 10 images
#> List of 10
#>  $ : num [1:128, 1:128] 0 0 0 0.00392 0 ...
#>  $ : num [1:128, 1:128] 0 0.00392 0.00392 0.00392 0 ...
#>  $ : num [1:128, 1:128] 0.00392 0.00392 0 0 0 ...
#>  $ : num [1:128, 1:128] 0 0 0 0.00392 0 ...
#>  $ : num [1:128, 1:128] 0 0 0.00392 0 0 ...
#>  $ : num [1:128, 1:128] 0 0 0.00392 0 0 ...
#>  $ : num [1:128, 1:128] 0 0.00392 0 0 0 ...
#>  $ : num [1:128, 1:128] 0 0 0 0.00392 0.00392 ...
#>  $ : num [1:128, 1:128] 0 0 0 0 0 ...
#>  $ : num [1:128, 1:128] 0 0 0 0.00392 0 ...
img[[1]][100:110, 101:105]  # print a section of the first image in the series
#>             [,1]       [,2]        [,3]        [,4]        [,5]
#>  [1,] 0.01176471 0.01176471 0.035294118 0.027450980 0.023529412
#>  [2,] 0.02352941 0.02745098 0.015686275 0.027450980 0.035294118
#>  [3,] 0.05490196 0.02352941 0.031372549 0.031372549 0.035294118
#>  [4,] 0.03921569 0.01568627 0.027450980 0.023529412 0.027450980
#>  [5,] 0.04313725 0.04313725 0.031372549 0.015686275 0.015686275
#>  [6,] 0.02352941 0.02352941 0.039215686 0.011764706 0.007843137
#>  [7,] 0.03137255 0.03529412 0.027450980 0.023529412 0.019607843
#>  [8,] 0.01960784 0.03921569 0.019607843 0.015686275 0.031372549
#>  [9,] 0.01568627 0.01960784 0.015686275 0.007843137 0.019607843
#> [10,] 0.05490196 0.04705882 0.019607843 0.035294118 0.023529412
#> [11,] 0.03137255 0.02352941 0.007843137 0.023529412 0.027450980

We just get 10 frames, with no information about the two channels.
We get annoying warnings about ImageJ’s private TIFF tags 50838 and 50839, which are of no interest to the R user.
The numbers in the image array(s) are (by default) normalized to the range [0, 1].

The `ijtiff` library

When we import the same image with the ijtiff library:

img <- ijtiff::read_tif(path_2ch_ij)
#> Reading a 128x128 pixel image of unsigned integer type with 2 channels and 5 frames.
dim(img)  # 2 channels, 5 frames
#> [1] 128 128   2   5
img[100:110, 101:105, 1, 1]  # print a section of the first channel, first frame
#>       [,1] [,2] [,3] [,4] [,5]
#>  [1,]    3    3    9    7    6
#>  [2,]    6    7    4    7    9
#>  [3,]   14    6    8    8    9
#>  [4,]   10    4    7    6    7
#>  [5,]   11   11    8    4    4
#>  [6,]    6    6   10    3    2
#>  [7,]    8    9    7    6    5
#>  [8,]    5   10    5    4    8
#>  [9,]    4    5    4    2    5
#> [10,]   14   12    5    9    6
#> [11,]    8    6    2    6    7

We see the image nicely divided into 2 channels of 5 frames.
We get no needless warnings.
The numbers in the image are integers, the same as would be seen if one opened the image with ImageJ.

ijtiff also includes a basic image display function:

ijtiff::display(img[, , 1, 1])  # first channel, first frame

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.

Floating point TIFFs

The original tiff package could read but not write floating point (real-numbered) TIFF files. The ijtiff library can do both. It automatically decides which type is appropriate when writing.

Advice for all ImageJ users

Base ImageJ (similar to the tiff R package) does not properly open some perfectly TIFF files¹ (including some TIFF files written by the tiff and ijtiff R packages). Instead it 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 BioFormats plugin. See https://imagej.net/Bio-Formats.

No support for volumetric, time based images

The package supports volumetric (\(z\)-stack) and time-based (time-stack) images, but not both volume and time simultaneously. The fourth slot in an ijtiff_img is either for \(z\) or time.

Text Images

TIFF files are limited in which numbers they can represent (they can’t go outside the 32-bit range). Real-numbered TIFFs can also lack precision, having only the precision of a 32-bit floating point number. If TIFF isn’t good enough, you can use text images.

library(ijtiff)
img[1] <- 2 ^ 99  # too high for TIFF
write_tif(img, "img")  # errors
#> Error in write_tif(img, "img"): The maximum value in 'img' is greater than 2 ^ 32 - 1 and therefore too high to be written to a TIFF file.
write_txt_img(img, "img")  # no problem

ijtiff

Rory Nolan

2017-12-19

Reading ImageJ TIFF files

The original `tiff` library

The `ijtiff` library

Note

Floating point TIFFs

Advice for all ImageJ users

No support for volumetric, time based images

Text Images

ijtiff

Rory Nolan

2017-12-19

Reading ImageJ TIFF files

The original tiff library

The ijtiff library

Note

Floating point TIFFs

Advice for all ImageJ users

No support for volumetric, time based images

Text Images

The original `tiff` library

The `ijtiff` library