Version 17.1 by mcpiastra on 2022/01/24 16:42
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rbakker 10.1 5 = Use case:
rbakker 13.1 6 Long-range projection neuron and 33 section images =
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mcpiastra 12.1 8 Pipeline performing coregistration of the neuron and the 2d-sections from which it was traced
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16 = What can I find here? =
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mcpiastra 14.1 18 This pipeline is dedicated to coregister 3D neuronal morphology traced in Neurolucida into the Allen atlas, making use of 2d-sections from which it was traced.
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mcpiastra 14.1 20 The pipeline consists of several steps:
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22 - neuron and image preprocessing;
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24 - projection of neuron-points into pixel coordinates in the associated experimental slice;
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mcpiastra 15.1 26 - QuickNII ([[https:~~/~~/ebrains.eu/service/quicknii-and-visualign/>>https://ebrains.eu/service/quicknii-and-visualign/]]) mapping between the atlas and the experimental slice;
mcpiastra 14.1 27
mcpiastra 15.1 28 -  Elastix ([[https:~~/~~/simpleelastix.github.io/>>https://simpleelastix.github.io/]]) coregistration of images and, consequently, neuron-points;
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30 - linear mapping of the reconstructed neuron into the original shape;
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32 - evaluation of the reconstructed neuron by comparison with the same neuron coregistered with a corresponding point technique, and with the ground truth extracted by the neuroanatomist.
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34 The code, intermediate and final results are stored in this collection.
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mcpiastra 8.2 36 = For whom is this interesting? =
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mcpiastra 14.1 38 Neuroscientists and neuroanatomists interested in ...
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44 {{box title="**Contents**"}}
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