Creating a tiff stack from individual tiffs in python

Question

I am creating tiff stacks of different sizes based on the example found here: http://www.bioimgtutorials.com/2016/08/03/creating-a-z-stack-in-python/

A sample of the tif files can be downloaded here: nucleus

I have a folder with 5 tiff files inside. I want to stack them to be able to open them in imageJ so that they look like this:

And this works with the following code:

from skimage import io
import numpy as np
import os

dir = 'C:/Users/Mich/Desktop/tiff stack/'

listfiles =[]


for img_files in os.listdir(dir):
    if img_files.endswith(".tif") :
        listfiles.append(img_files)



first_image = io.imread(dir+listfiles[0])

io.imshow(first_image)

first_image.shape

stack = np.zeros((5,first_image.shape[0],first_image.shape[1]),np.uint8)



for n in range(0,5):
    stack[n,:,:]= io.imread(dir+listfiles[n])

path_results = 'C:/Users/Mich/Desktop/'
io.imsave(path_results+'Stack.tif' ,stack)

The problem comes when I just want to stack the 4 first ones or the 3 first ones.

Example with 4 tiff images:

   stack=np.zeros((4,first_image.shape[0],first_image.shape[1]),np.uint8)

   for n in range(0,4):
       stack[n,:,:]= io.imread(dir+listfiles[n])

Then I obtain this kind of result:

and while trying to stack the 3 first images of the folder, they get combined!

   stack=np.zeros((3,first_image.shape[0],first_image.shape[1]),np.uint8)

   for n in range(0,3):
       stack[n,:,:]= io.imread(dir+listfiles[n])

Where am I wrong in the code, so that it dosent just add the individual tiff in a multidimensional stack of the sizes 3, 4 or 5 ?

Answer 1

Specify the color space of the image data (photometric='minisblack'), otherwise the tifffile plugin will guess it from the shape of the input array.

This is a shorter version using tifffile directly:

import glob
import tifffile

with tifffile.TiffWriter('Stack.tif') as stack:
    for filename in glob.glob('nucleus/*.tif'):
        stack.save(
            tifffile.imread(filename), 
            photometric='minisblack', 
            contiguous=True
        )