Version 19.3 by rbakker on 2022/01/24 16:49
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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;
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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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rbakker 19.2 38 Neuroscientists and neuroanatomists working with neuronal morphologies and who would like to register their data to an atlas. In particular the Allen mouse atlas is very interesting because large numbers of neurons are already available in that space from two large initiatives: Mouselight ([[https:~~/~~/www.janelia.org/project-team/mouselight>>https://www.janelia.org/project-team/mouselight]]) and Braintell ([[https:~~/~~/doi.org/10.35077/g.25>>https://doi.org/10.35077/g.25]]).
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44 {{box title="**Contents**"}}
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