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1	1	== (% style="color:#c0392b" %)How can I identify brain regions in my images?(%%) ==
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3	3	(% class="wikigeneratedid" %)
4		-By using QuickNII, you will be able to register this image series to the mouse reference atlas version of your choice and obtain adapted atlas maps and coordinates. Further, in-plane non-linear adjustments can be made with VisuAlign in order to obtain a more precise registration. The regions shown in the example below are color coded and correspond to Mouse CCFv3_2017 atlas^^1^^ .
	4	+By using QuickNII, you will be able to register this image series to the mouse reference atlas version of your choice and obtain adapted atlas maps and coordinates. Further, in-plane non-linear adjustments can be made with VisuAlign in order to obtain a more precise registration. The regions shown in the example below are color coded and correspond to Mouse CCFv3_2017 atlas ( Oh et al. 2014).
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6	6	(% class="wikigeneratedid" id="H" %)
7	7	(% style="color:#c0392b" %)[[image:Doublet_illust_NOP_tta.png]]
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10	10	== (% style="color:#c0392b" %)How can I map the position of my reconstructed neuron?(%%) ==
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12		-After in-vivo electrophysiology experiments, the recorded neurons are filled with neurobiotin making them visible on histological images. These images are registered to the Mouse atlas CCFv3_2017^^1^^. The extracted coordinates of the neuron soma and the coordinates of the neuronal arbor, could then be mapped in the 3D reference space.
	12	+After in-vivo electrophysiology experiments, the recorded neurons are filled with neurobiotin making them visible on histological images. These images are registered to the Mouse atlas CCFv3_2017 ( Oh et al. 2014). The extracted coordinates of the neuron soma and the coordinates of the neuronal arbor, could then be mapped in the 3D reference space.
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16		-(% style="text-align:center" %)
17		-[[image:QNII_neuron_recons.png||height="600" width="565"]]
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19		-(% class="wikigeneratedid" %)
20		-Image from Bjerke et al. 2018. //Front. Neuroinform.// 12:82. [[doi:10.3389/fnana.2018.00082>>https://www.frontiersin.org/articles/10.3389/fnana.2018.00082/full]]
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22	22	== (% style="color:#c0392b" %)How can I count my labelled cells?(%%) ==
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32	32	== (% style="color:#c0392b" %)How can I map the position of my electrode?(%%) ==
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37		-~1. (Oh et al. 2014)