I am trying to save an altered z-stack .tif file in Python3. Here's my code where I checked that the the functions worked as intended. #libraries import imageio as ii #import initial image fname='101_nuc1syg1.tif' adata = ii.volread(fname) #check to make sure volread works ii.volsave('temp.tif', adata) Which results in this: And now when I try to do a simple threshold, using the following code: #now doing very simple thresholding bdata = adata < adata[0].mean() bdata = bdata +0 ii.volsave('temp.tif', bdata) I get this: Any idea how to save a tif file properly after performing image operators on it? EDIT: Note that I am able to extract each stack and save them as separate .png files, but I would prefer to have them as a single .tif file. Data from: https://www.nature.com/articles/s41467-020-15987-2 Continue reading...