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2	2	(((
3	3	(% class="container" %)
4	4	(((
5		-= Use case:
6		-Long-range projection neuron and 33 section images =
	5	+= Coregistration of a neuron and the 2d-sections from which it was traced =
7	7
8		-Pipeline performing coregistration of the neuron and the 2d-sections from which it was traced
	7	+Coregistration of a neuron and the 2d-sections from which it was traced
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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.
	17	+* Notice how the table of contents on the right
	18	+* is automatically updated
	19	+* 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 mapping between the atlas and the experimental slice;
27		-
28		--  Elastix 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 ...
	23	+Describe the audience of this collab.
39	39	)))
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