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NumPy and Tensorflow implementation of the Multidimensional Contrast Limited Adaptive Histogram Equalization (MCLAHE) procedure

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Multidimensional Contrast Limited Adaptive Histogram Equalization

Introduction

Sample datasets

Fluorescence microscopy

Fluorescence microscopy can be used to capture time resolved volumetric images of a developing embryo. To illustrate the effectiveness of MCLAHE we applied it to a dataset of an organism of species phallusia mammillata (available here). To reduce the noise in the data, we preprocessed it by a median filter with kernel size (2, 2, 2, 1) in the (x, y, z, t) space

MCLAHE applied to fluorescence microscopy data

The above image show a slice along the z-axis through the data. 4D CLAHE clearly enhances the contrast of the data. Our hyperparameters of choice were the kernel size (20, 20, 10, 25), 256 bins in the histogram, and a clipping limit of 0.25. We used a global histogram range

Multidimensional photoemission spectroscopy

Multidimensional photoemission spectroscopy is a technique to map the electronic band structure in a 4D space consisting of two momentum (kx, ky), an energy (E), and a time (t) coordinate. In the raw data, the excited state (E > 0) is not visible. 4D CLAHE makes is visible while enhancing local features in the other states but preserving the temporal intensity changes.

MCLAHE applied to MPES data

Here, we used a kernel size of (30, 30, 15, 20) in (kx, ky, E, t) space, 256 histogram bins, and a clipping limit of 0.02. We made use of the adaptive histogram range for processing this dataset.

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NumPy and Tensorflow implementation of the Multidimensional Contrast Limited Adaptive Histogram Equalization (MCLAHE) procedure

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