Saving .tif Image Incorrectly using Python3 and imageio

Question

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

Answer 1

It looks like you need to convert bdata type to np.uint8 and multiply the result by 255.

• The type of the expression (adata < adata[0].mean()) is np.bool.
  The common image type is np.uint8.
  Convert (adata < adata[0].mean()) to type np.uint8:

   bdata  = (adata < adata[0].mean()).astype(np.uint8)
  

• When converting the result to np.uint8, all True elements are converted to 1 and False elements are converted to 0.
  Multiply by 255 for converting the True elements to 255 (white color):

   bdata = bdata * 255
  

---

Complete code:

import imageio as ii
import numpy as np

#import initial image
fname='101_nuc1syg1.tif'
adata = ii.volread(fname)

#now doing very simple thresholding
bdata  = (adata < adata[0].mean()).astype(np.uint8)

bdata = bdata * 255  # Convert ones to 255 (255 is white color)

ii.volsave('temp.tif', bdata)

Note:
I could not test my answer - the link you have posted doesn't contain a link to an image.