Raju, Rajeswari
(2016)
Optimisation of image processing networks for neuronal membrane detection.
PhD thesis, University of Nottingham.
Abstract
This research dealt with the problem of neuronal membrane detection, in which the core challenge is distinguishing membranes from organelles. A simple and efficient optimisation framework is proposed based on several basic processing steps, including local contrast enhancement, denoising, thresholding, hole-filling, watershed segmentation, and morphological operations. The two main algorithms proposed Image Processing Chain Optimisation (IPCO) and Multiple IPCO (MIPCO)combine elements of Genetic Algorithms, Differential Evolution, and Rank-based uniform crossover. 91.67% is the highest recorded individual IPCO score with a speed of 280 s, and 92.11% is the highest recorded ensembles IPCO score whereas 91.80% is the highest recorded individual MIPCO score with a speed of 540 s for typically less than 500 optimisation generations and 92.63% is the highest recorded ensembles MIPCO score.Further, IPCO chains and MIPCO networks do not require specialised hardware and they are easy to use and deploy. This is the first application of this approach in the context of the Drosophila first instar larva ventral nerve cord. Both algorithms use existing image processing functions, but optimise the way in which they are configured and combined. The approach differs from related work in terms of the set of functions used, the parameterisations allowed, the optimisation methods adopted, the combination framework, and the testing and analyses conducted. Both IPCO and MIPCO are efficient and interpretable, and facilitate the generation of new insights. Systematic analyses of the statistics of optimised chains were conducted using 30 microscopy slices with corresponding ground truth. This process revealed several interesting and unconventional insights pertaining to preprocessing, classification, post-processing, and speed, and the appearance of functions in unorthodox positions in image processing chains, suggesting new sets of pipelines for image processing. One such insight revealed that, at least in the context of our membrane detection data, it is typically better to enhance, and even classify, data before denoising them.
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