Last modified by rbakker on 2022/05/23 22:23
From version 8.2
edited by mcpiastra
on 2021/12/17 16:54
Change comment: There is no comment for this version
To version 16.1
edited by mcpiastra
on 2022/01/24 16:42
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= Coregistration of a neuron and the 2d-sections from which it was traced =
5 += Use case:
6 +Long-range projection neuron and 33 section images =
6 6  
7 -Coregistration of a neuron and the 2d-sections from which it was traced
8 +Pipeline performing coregistration of the neuron and the 2d-sections from which it was traced
8 8  )))
9 9  )))
10 10  
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14 14  (((
15 15  = What can I find here? =
16 16  
17 -* Notice how the table of contents on the right
18 -* is automatically updated
19 -* to hold this page's headers
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.
20 20  
20 +The pipeline consists of several steps:
21 +
22 +- neuron and image preprocessing;
23 +
24 +- projection of neuron-points into pixel coordinates in the associated experimental slice;
25 +
26 +- QuickNII ([[https:~~/~~/ebrains.eu/service/quicknii-and-visualign/>>https://ebrains.eu/service/quicknii-and-visualign/]]) mapping between the atlas and the experimental slice;
27 +
28 +-  Elastix ([[https:~~/~~/simpleelastix.github.io/>>https://simpleelastix.github.io/]]) coregistration of images and, consequently, neuron-points;
29 +
30 +- linear mapping of the reconstructed neuron into the original shape;
31 +
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.
33 +
34 +The code, intermediate and final results are stored in this collection.
35 +
21 21  = For whom is this interesting? =
22 22  
23 -Describe the audience of this collab.
38 +Neuroscientists and neuroanatomists interested in ...
24 24  )))
25 25  
26 26  
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