Wiki source code of Atlas registration of neuronal morphologies obtained from mouse brain sections

Version 17.1 by mcpiastra on 2022/01/24 16:42

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10.1	5	= Use case:
13.1	6	Long-range projection neuron and 33 section images =
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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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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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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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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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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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8.2	36	= For whom is this interesting? =
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14.1	38	Neuroscientists and neuroanatomists interested in ...
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