import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt

img = np.zeros((100, 400))
img[::5, ::5] = 1
idx = np.indices(img.shape)
idx = [idx[0][::5].flatten(), idx[1][:, ::5].flatten()]

fig, ax = plt.subplots(constrained_layout=True)
ax.imshow(img, interpolation="None", origin="lower")
ax.scatter(idx[1], idx[0], marker="x", lw=0.2, s=1)
fig.savefig("imshow.pdf")

class NotRoundedAxesImage(mpl.image.AxesImage):
    """AxesImage subclass which does not round image extents to fit frame

    This rounding leads to improper alignment between data and image
    """
    def make_image(self, renderer, magnification=1.0, unsampled=False):
        # docstring inherited
        trans = self.get_transform()
        # image is created in the canvas coordinate.
        x1, x2, y1, y2 = self.get_extent()
        bbox = mpl.transforms.Bbox(np.array([[x1, y1], [x2, y2]]))
        transformed_bbox = mpl.transforms.TransformedBbox(bbox, trans)
        clip = ((self.get_clip_box() or self.axes.bbox) if self.get_clip_on()
                else self.figure.bbox)
        # Turn off round_to_pixel_border!
        return self._make_image(self._A, bbox, transformed_bbox, clip,
                                magnification, unsampled=unsampled,
                                round_to_pixel_border=False)
    
fig, ax = plt.subplots(constrained_layout=True)
# Replicate Axes.imshow
ax.set_aspect(mpl.rcParams["image.aspect"])
ai = NotRoundedAxesImage(ax, interpolation="none")
ai.set_data(img)
ai.set_extent(ai.get_extent())
ax.add_image(ai)
ax.scatter(idx[1], idx[0], marker="x", lw=0.2, s=1)
fig.savefig("custom_image.pdf")