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1	1	== (% style="color:#c0392b" %)How can I identify brain regions in my images?(%%) ==
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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).
	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^^ .
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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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	9	+(% class="small" %)Histological data available on EBRAINS: [[DOI 10.25493/AYBB-BXV>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset&q=neuropsin#Dataset/d56b1fe14bb84987a3a2340e21652b2d]]
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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 (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.
	13	+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.
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16		-[[image:QNII_neuron_recons.png]]
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	18	+[[image:QNII_neuron_recons.png||height="600" width="565"]]
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	21	+(% class="small" %)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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	24	+(% class="small" %)Electrophysiological data available on EBRAINS: DOI: [[10.25493/ADRK-VJP>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset&q=grillner#Dataset/749eab9b-3159-4eb8-a36b-85757208e3c1]]
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18	18	== (% style="color:#c0392b" %)How can I count my labelled cells?(%%) ==
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23	23	[[image:Figure4.jpg]]
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25		-Image from Groeneboom NE, Yates SC, Puchades MA and Bjaalie JG (2020) Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. //Front. Neuroinform.// 14:37. doi: [[10.3389/fninf.2020.00037>>url:https://www.frontiersin.org/articles/10.3389/fninf.2020.00037/full]]
	33	+(% class="small" %)Image from Groeneboom NE, Yates SC, Puchades MA and Bjaalie JG (2020) Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. //Front. Neuroinform.// 14:37. doi: [[10.3389/fninf.2020.00037>>url:https://www.frontiersin.org/articles/10.3389/fninf.2020.00037/full]]
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28		-== (% style="color:#c0392b" %)How can I map the position of my electrode?(%%) ==
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	39	+~1. (Oh, S. W., Harris, J. A., Ng, L., Winslow, B., Cain, N., Mihalas, S., et al. (2014). A mesoscale connectome of the mouse brain. Nature 508, 207–214. doi: 10.1038/nature13186)