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    <pre><code>import numpy as np import scipy import scipy.ndimage as ndimage import scipy.ndimage.filters as filters import matplotlib.pyplot as plt fname = '/tmp/slice0000.png' neighborhood_size = 5 threshold = 1500 data = scipy.misc.imread(fname) data_max = filters.maximum_filter(data, neighborhood_size) maxima = (data == data_max) data_min = filters.minimum_filter(data, neighborhood_size) diff = ((data_max - data_min) &gt; threshold) maxima[diff == 0] = 0 labeled, num_objects = ndimage.label(maxima) slices = ndimage.find_objects(labeled) x, y = [], [] for dy,dx in slices: x_center = (dx.start + dx.stop - 1)/2 x.append(x_center) y_center = (dy.start + dy.stop - 1)/2 y.append(y_center) plt.imshow(data) plt.savefig('/tmp/data.png', bbox_inches = 'tight') plt.autoscale(False) plt.plot(x,y, 'ro') plt.savefig('/tmp/result.png', bbox_inches = 'tight') </code></pre> <p>Given <strong>data.png</strong>:</p> <p><img src="https://i.stack.imgur.com/rdEYd.png" alt="enter image description here"></p> <p>the above program yields <strong>result.png</strong> with <code>threshold = 1500</code>. Lower the <code>threshold</code> to pick up more local maxima:</p> <h2><img src="https://i.stack.imgur.com/86XgT.png" alt="enter image description here"></h2> <p><strong>References</strong>:</p> <ul> <li><a href="https://stackoverflow.com/a/5304140/190597">J.F. Sebastian counts nuclei</a> </li> <li><a href="https://stackoverflow.com/questions/4087919/how-can-i-improve-my-paw-detection">Joe Kington finds paw prints</a></li> <li><a href="https://stackoverflow.com/a/3689710/190597">Ivan finds local maximums</a></li> </ul>
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    1. POGet coordinates of local maxima in 2D array above certain value
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    1. USunutbu
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    1. POGet coordinates of local maxima in 2D array above certain value
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    1. COhello unutbu, I'm afraid I don't really get your solution, meaning the output. at the moment I managed to kick out all maxima that have absolute value less than let's say 1500. I'm just trying if the outcome is satisfying.
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    2. COMost likely it is I who does not understand your question. Are you looking for a way to find the `(x,y)` coordinates of the maxima? If so, you can find them using `np.where(maxima)`.
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    3. COyou're right. but I want to get rid of the local maxima being in the background. like saying: a local maximum is only a local maximum if it stands out from its neighborhood more than a certain value. At the moment I cancel the background by setting all pixels to zero that have a value below 1500, but I am not really satisfied with this. Do you know ImageJ? The 'Find Maxima' function does a pretty good job and I'd like to reproduce this output. To be clear: I want to have the coordinates of the brightest pixels within the bright spots on the picture.
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