Last modified by rbakker on 2022/05/23 22:23
From version 18.1
edited by mcpiastra
on 2022/01/24 16:42
Change comment: There is no comment for this version
To version 10.1
edited by rbakker
on 2021/12/17 16:56
Change comment: There is no comment for this version

Summary

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Author
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1 -XWiki.mcpiastra
1 +XWiki.rbakker
Content
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3 3  (% class="container" %)
4 4  (((
5 5  = Use case:
6 -Long-range projection neuron and 33 section images =
6 +traced neuron and 33 section images =
7 7  
8 -Pipeline performing coregistration of the neuron and the 2d-sections from which it was traced
8 +Pipelinne performing coregistration of the neuron and the 2d-sections from which it was traced
9 9  )))
10 10  )))
11 11  
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15 15  (((
16 16  = What can I find here? =
17 17  
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.
18 +* Notice how the table of contents on the right
19 +* is automatically updated
20 +* to hold this page's headers
19 19  
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 -
36 36  = For whom is this interesting? =
37 37  
38 -Neuroscientists and neuroanatomists interested in ...
24 +Describe the audience of this collab.
39 39  )))
40 40  
41 41  
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