Incorrect image dimensions after reading in 3D+c TIFF

I’m trying to read the following file:

https://www.dropbox.com/s/0ynbscx4cmd5k91/E_z2_512_1um_CONTROL.tif?dl=1

skimage (ie tifffile) reads this correctly, but imageio doesn’t — even though I thought it also used tifffile as a backend for tiffs?

In [1]: import imageio
In [2]: from skimage import io
In [3]: im_iio = imageio.imread('E_z2_512_1um_CONTROL.tif')
In [4]: im_iio.shape
Out[4]: (159, 320, 512)

In [5]: im_ski = io.imread('E_z2_512_1um_CONTROL.tif')
In [6]: im_ski.shape
Out[6]: (53, 320, 512, 3)

What imageio is doing is reading the file in the array order present in the file (plane, channel, row, column), and squashing pln and ch dimensions together, while skimage is behaving as expected and producing two separate dimensions for pln and ch and (maybe a bit more than expected) moving ch to the last dimension, which is the dimension order expected by most scipy packages.

Any ideas about what is going wrong here?

[blink1073]

I’d say adopt the skimage convention.

[almarklein]

Attempt at a fix: #255