I want to remove 1 color channel from a tif in zcyx and save it in zyx

Question

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

Please put your `import` statements back in so we know what packages you are using, so it is a proper [mcve]. — Mark Setchell, Jul 25 '23 at 18:48
Either keep the channel axis `TifIm[:,1:2,:,:]` or specify the axes in `imwrite(..., metadata={'axes': 'ZYX'}`). — cgohlke, Jul 25 '23 at 20:33
Please provide enough code so others can better understand or reproduce the problem. — Community, Jul 25 '23 at 21:21

score 1 · Answer 1 · edited Jul 30 '23 at 11:27

1

Update: Thank you to cgohlke. Specifying the axes in the metadata has done the trick.

tif.imwrite(Image + "_Red.ome.tif",SplitRed,imagej= True,metadata= {'axes': 'ZYX'})

Thank you everyone and sorry for being vague

edited Jul 30 '23 at 11:27

Born2Smile

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answered Jul 26 '23 at 19:38

Mohammed Hijaz

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I want to remove 1 color channel from a tif in zcyx and save it in zyx

1 Answers1