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1		-XWiki.puchades
	1	+XWiki.evanhancock

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1	1	== [[image:BICCN_QNII_figure.png]] ==
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3		-(% class="wikigeneratedid" id="H-1" %)
4		-Image registration using QuickNII
	3	+== ==
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8	8	The QUINT workflow allows you to register series of histological section images from the brain to a 3D reference atlas such as the Allen Mouse Brain Atlas or the Waxholm Space atlas of the rat brain. This is a two-step process:
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10	10	1. QuickNII guides you through an interactive affine alignment, including propagation of alignment settings across the section series.
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25	25	(% style="color:#4e5f70" %)Open the //QuickNII// program from the .exe file. Once the program opens, click the **Manage data button** and load your XML file.
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27		-A detailed //QuickNII// user manual as well as a demo dataset [[can be found here>>https://www.nitrc.org/docman/?group_id=1341]].
	24	+A detailed //QuickNII// user manual as well as a demo dataset [[can be found here>>https://www.nitrc.org/projects/quicknii/]].
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29	29	== (% style="color:#c0392b" %)**Anchoring procedure**(%%) ==
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65	65	1. You can toggle “outline mode” by pulling the opacity slider to the far right. A colour picker on the right side of the slider becomes active for changing the outline colour.
66	66	1. Enabling “Debug mode” from the View menu toggles the display of triangles representing the deformation field, and allows you to change the colour of the triangles.
67	67	1. Finally, use File -> Save As to save your fine-tuned alignment as a new JSON file.
68		-1. There is also an “Export”function for generating .flat files for Nutil.