I though it would be as simple as picking 1 color and keeping the rest of the axis the same. from tkinter import filedialog import tifffile as tif import os def SplitChannel(ImName): TifIm = tif.imread(ImName) return TifIm[:,1,:,:] #for some reason this makes the tiff read cyx vs zyx if __name__ == "__main__": Folder = filedialog.askdirectory(title = "Select the directory containing Tif files") ImageNames = os.listdir(Folder) SaveFolder = Folder + " Split Red Channel2" os.mkdir(SaveFolder) os.chdir(Folder) for Image in ImageNames: if Image.split(".")[-1] == "tif": print("here") SplitRed = SplitChannel(Image) os.chdir("...") os.chdir(SaveFolder) tif.imwrite(Image + "_Red.ome.tif",SplitRed,imagej= True) os.chdir("...") os.chdir(Folder) But this gives me a tif in cyx vs zyx. How can I make sure the resulting tif knows I removed a color channel, and not z Continue reading...