How to remove gaps between image subplots

You can set the height_ratios of the subplots using the gridspec_kw argument in the call to plt.subplots, and use the heights of the different images to set that ratio.

From the docs to plt.subplots():

gridspec_kw : dict, optional

Dict with keywords passed to the GridSpec constructor used to create the grid the subplots are placed on.

Note that your example had the exact aspect ratio of the default matplotlib image size, so you wouldn’t notice any gaps appearing until you add more rows, or change the shapes of the images.

So, to expand this to a general solution, you will need to set the figure size according to the shapes of the images. For example, lets expand your example to 3 rows, 2 columns. We’ll also explicitly set the figure width to 8 inches, and adjust the height based on the image sizes.

from numpy.random import rand
import matplotlib.pyplot as plt

test_data = [[rand(10,10), rand(10,10)],[rand(5,10), rand(5,10)],[rand(2,10), rand(2,10)]]
cmaps = [['viridis', 'binary'], ['plasma', 'coolwarm'], ['Greens', 'copper']]

heights = [a[0].shape[0] for a in test_data]
widths = [a.shape[1] for a in test_data[0]]

fig_width = 8.  # inches
fig_height = fig_width * sum(heights) / sum(widths)

f, axarr = plt.subplots(3,2, figsize=(fig_width, fig_height),
        gridspec_kw={'height_ratios':heights})

for i in range(3):
    for j in range(2):
        axarr[i, j].imshow(test_data[i][j], cmap=cmaps[i][j])
        axarr[i, j].axis('off')
plt.subplots_adjust(wspace=0, hspace=0, left=0, right=1, bottom=0, top=1)
plt.show()