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Convert MHD format to PNG image

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The MHD file is an ITK Meta-Image Header.

Insight Segmentation and Registration Toolkit (ITK) is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis.

Tested in Anaconda and Python 3.7

import SimpleITK as sitk
import matplotlib.pylab as plt
 
ct_scans = sitk.GetArrayFromImage(sitk.ReadImage("70-air-body-lungs.mhd", sitk.sitkFloat32))
 
for i in range(ct_scans.shape[0]):
    plt.imshow(ct_scans[i], 'gray')
    plt.axis('off')
    plt.show()
    plt.imsave('output/70-air-body-lungs_' + str(i) + '.png', ct_scans[i], cmap='gray', format='png')

mhd2png

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Downloading the 70-air-body-lungs.mhd and 70-air-body-lungs.raw files

Distribution of software for the processing and analysis of scientific images

The toolkit for scientific image processing and analysis

Fiji distribution of ImageJ

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