Read and write 3D RGB tiff stacks
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.
writeTIF(cell, file="my_cell.tif")
## [1] 52
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
Plotting
img() is a plotting function for images stored in an
array.
par(pty="s")
bioimagetools::img(cell, z=25, col="rgb")
bioimagetools::img(cell, z=25, col="r")
bioimagetools::img(cell, z=25, col="grey")
Reading Bitmap files
Simple Bitmap files can be imported by readBMP().
bi<-readBMP(system.file(package = "bioimagetools","extdata", "V.bmp"))
par(pty="s")
image(bi, col=grey(seq(0,1,length=2^8)))
Single TIF slices
In order to work with single slices, you would like to select the
slice from the array:
However, this will result in the wrong dimension. bioimagetools
always needs 4d array:
dim(slice30) # only 3d
## [1] 512 512 3
dim(slice30) <- c(dim(slice30), 1)
dim(slice30) # 4d
## [1] 512 512 3 1
img(slice30, z=1, col="rgb")
writeTIF(slice10,paste0("slice30.tif"))
## [1] 1
To read single RGB slices, you can use readTIFF. Make sure to add the
option channels=3 for an RGB slice.
slice30<-readTIF("slice30.tif", channels=3)
dim(slice30)
## [1] 272 270 3 1
To stack single slices use abind from the abind package:
for (i in 1:52)writeTIF(cell[,,,i],paste0("slice",i,".tif")) # write slices
slice<-list()
for (i in 1:52)slice[[i]]<-readTIF(paste0("slice",i,".tif"), channels=3) # read slices
allslices<-slice[[1]] # slice 1
for (i in 2:52)allslices<-abind::abind(allslices, slice[[i]]) # stack slices 2 to 52
dim(allslices)
## [1] 512 512 3 52
The attributes will be off for the stacked array, so we need to add
them from hand using one of the slices (not the dimension!):
attrib<-attributes(slice[[1]])
attrib<-attrib[names(attrib)!="dim"] # Remove dimension attribute
attributes(allslices)<-c(attributes(allslices),attrib)