readTIF()
and writeTIF()
read and write tiff stacks.
3D and color stacks are automatically recognized by readTIF()
, if the meta information is correct. Available meta information is saved as attributes. readTIF()
can also handle URLs. The function returns an array with range 0 to 1.
cell <- bioimagetools::readTIF("http://ex.volkerschmid.de/cell.tif")
## Warning in tiff::readTIFF(file, all = TRUE, info = TRUE, as.is = as.is, :
## TIFFReadDirectory: Unknown field with tag 50838 (0xc696) encountered
## Warning in tiff::readTIFF(file, all = TRUE, info = TRUE, as.is = as.is, :
## TIFFReadDirectory: Unknown field with tag 50839 (0xc697) encountered
print(dim(cell))
## [1] 512 512 3 52
print(attributes(cell)$dim)
## [1] 512 512 3 52
print(attributes(cell)$bits.per.sample)
## [1] 16
par(pty="s")
bioimagetools::img(cell, z=25 ,col="rgb")
writeTIF()
writes out tiff stacks. Meta information in attributes are saved. The bits per sample can be controlled by an option.
readClassTIF()
is a special version of readTIF()
for images with a very low number of intensity values, e.g. masks or segmented images.
bioimagetools::writeTIF(2*EBImage::thresh(cell[,,1,])+EBImage::thresh(cell[,,2,]), file="simple.tif")
## [1] 52
mysimple <- readClassTIF("simple.tif", n=3)
par(pty="s")
bioimagetools::img(mysimple[,,25],col="red",up=3)
## [1] TRUE
## [1] TRUE
img()
is a plotting function for images stored in an array.