Summary

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Author

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1		-XWiki.rbakker
	1	+XWiki.mcpiastra

Content

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3	3	(% class="container" %)
4	4	(((
5	5	= Use case:
6		-traced neuron and 33 section images =
	6	+Long-range projection neuron and 33 section images =
7	7
8		-Pipelinne performing coregistration of the 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
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15	15	(((
16	16	= What can I find here? =
17	17
18		-* Notice how the table of contents on the right
19		-* is automatically updated
20		-* 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.
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	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	+
22	22	= For whom is this interesting? =
23	23
24		-Describe the audience of this collab.
	38	+Neuroscientists and neuroanatomists interested in ...
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