Maximum intensity projection from image stack

Question

I'm trying to recreate the function

max(array, [], 3)

From MatLab, which can take my 300x300px image stack of N images (I'm saying "Image" here because I'm processing images, really this is just a big double array), 300x300xN, and create a 300x300 array. What I think is happening in this function, if it were to operate inefficiently, is that it is parsing through each (x,y) point, then taking the maximum value from that point across the z-axis, then normalizing with maximum and minimum values of the entire array.

I've tried recreating this in python with

# Shape of dataset: (300, 300, 181)
# Type of dataset: <type 'numpy.ndarray'>
for x in range(numpy.size(self.dataset, 0)):
    for y in range(numpy.size(self.dataset, 1)):
        print "Point is", x, y
        # more would go here to find the maximum (x,y) value over Z axis in self.dataset

A very simple X,Y iterator. -- but not only does my IDE crash after a few milliseconds of running this code, but also it feels gross and inefficient.

Is there something I'm missing? I'm new to Python, and therefore the answer here isn't clear to me. Is there an existing function that does this operation?

You should post in the question a small sample dataset, say of dimensions 10*10*3, which will help others to give suggestions. — rnso
– rnso, Commented Jan 10, 2018 at 1:27
I thought your problem with return self.dataset array size. can you try this, please? dim1 = len(self.dataset) dim2 = len(self.dataset[0]) dim3 = len(self.dataset[0][0]) to get right array dimintions. — Mohammad nagdawi
– Mohammad nagdawi, Commented Jan 10, 2018 at 1:38
MATLAB's max does not normalize. It just takes the maximum, in this case, of array(i,j,:) for each combination of i and j. — Cris Luengo
– Cris Luengo, Commented Jan 10, 2018 at 1:58
The Numpy equivalent of max(array, [], 3) would be np.amax(array, axis=2). There's no normalization in either function. — buzjwa
– buzjwa, Commented Jan 10, 2018 at 11:00

Seyed Mostafa Mousavi Kahaki · Accepted Answer · 2018-08-29 20:16:40Z

13

import numpy as np
import matplotlib.pyplot as plt
from skimage import io

path = "test.tif"
IM = io.imread(path)
IM_MAX= np.max(IM, axis=0)
plt.imshow(IM_MAX)

answered Aug 29, 2018 at 20:16

Seyed Mostafa Mousavi Kahaki

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1 Comment

user115625 Over a year ago

@kai no, the original answer is correct. skimage reads the image axis as (plane, row, column) so axis=0 is the plane which is the z-axis.

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