Why isn't imshow displaying correctly when using custom ticks?

I am trying to plot heatmap with average values with x and y axes denote physical parameters.

import csv
import matplotlib.pyplot as plt
from scipy import stats
import numpy as np

#.......................................................................
# URL for temp.csv https://github.com/paragkan/dyanmic-recrystallization/blob/main/temp.csv
#.......................................................................
def read_csv(xfile):
    infile = open(xfile, 'r')
    table = []
    for row in csv.reader(infile):
        table.append(row)
    infile.close() # better leave that file alone.
    for c in range (0, len(table[0])):
        for r in range(0, len(table)):
            try:
                table[r][c] = float(table[r][c])
            except:
                pass
    return table
#.......................................................................

xfile = 'temp.csv'

table = read_csv(xfile)

x = []
y = []
z = []

for i in range(0, len(table)):
    x.append(int(1/table[i][0]))
    y.append(table[i][1])
    z.append(table[i][2])

extent = [min(x), max(x), min(y), max(y)]
d = stats.binned_statistic_2d(x, y, z, statistic='mean', bins = [5, 5])

fig, ax = plt.subplots()
extent = [min(x), max(x), min(y), max(y)]
# im = ax.imshow(d[0].T, cmap='RdBu_r',  interpolation='nearest', origin='lower', extent=extent)
im = ax.imshow(d[0].T, cmap='RdBu_r',  interpolation='nearest', origin='lower')

print(d[0])
print(d[1])
print(d[2])

# ax.set_xticks(d[1])
# ax.set_yticks(d[2])

cbar = ax.figure.colorbar(im, ax = ax, shrink = 1)
# average = d[0].T
# xdist = d[1]
# ydist = d[2]
# for i in range(0, len(d[1])-1):
#     for j in range(len(d[2])-1):
#         xcord = (xdist[j] + xdist[j+1])/2
#         ycord = (ydist[i] + ydist[i+1])/2
#         txtext = plt.text(xcord, ycord, round(average[i][j], 2),  fontsize = 12, ha="center", va="center", color="w")
plt.show()
plt.close()

Printed Output

[[0.00658065 0.01352    0.03897    0.09360667 0.15375806]
 [       nan        nan        nan        nan        nan]
 [0.00704516 0.02388    0.11518667 0.37206333 0.69959677]
 [       nan        nan        nan        nan        nan]
 [0.00575484 0.01212    0.05937667 0.22448333 0.46173226]]
[ 923.   962.8 1002.6 1042.4 1082.2 1122. ]
[ 2.83236704  4.58410957  6.33585211  8.08759464  9.83933718 11.59107971]

Without extent

With extent=extent

When I use 'extent' parameter or custom axes ticks using set_xticks, the map is not showing correctly. Without 'extent', everything is fine but then the axes ticks are indexed as 0, 1, 2, 3. Kindly help me resolve this issue. It is also OK if someone suggests another python package to plot heatmap with binned stats, I require saved graphs to be used in a manuscript.

Expected Plot

What I need is, the edges of the bins in the graph should show the actual bin's dimension. If xedges are = [900, 925, 975, ..], the ticks on the x-axis should start with 900, and the next tick should be on the next bin edge showing 925. The same for y-axis.

temp.csv

8.90472E-4,2.8323670382,0.0054
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8.90472E-4,3.7024378338,0.0056
8.90472E-4,3.7604425536,0.0057
8.90472E-4,3.8184472733,0.0057
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You can use the "aspect" option in imshow to force the image to return to the correct aspect ratio. To get a square image, the aspect ratio would need to be the inverse of the ratio of the two side lengths. See also: https://stackoverflow.com/questions/13384653/imshow-extent-and-aspect

In your case your x length is about 200 and your y length is about 10, so you'd want to set an aspect of about 20.