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1	1	== [[image:BICCN_QNII_figure.png]] ==
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3		-== ==
	3	+(% class="wikigeneratedid" id="H-1" %)
	4	+(% class="small" %)Section image registration using QuickNII
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5	5	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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7	7	1. QuickNII guides you through an interactive affine alignment, including propagation of alignment settings across the section series.
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22	22	(% 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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24		-A detailed //QuickNII// user manual as well as a demo dataset can be found on [[https:~~/~~/www.nitrc.org/projects/quicknii/>>https://www.nitrc.org/projects/quicknii/]]
	27	+A detailed //QuickNII// user manual as well as a demo dataset [[can be found here>>https://www.nitrc.org/docman/?group_id=1341]].
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26	26	== (% style="color:#c0392b" %)**Anchoring procedure**(%%) ==
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53	53	**[[image:VisuAlign_illustration.png]]**
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55		- A detailed //VisuAlign //user manual can be found on [[https:~~/~~/www.nitrc.org/docman/?group_id=1426>>https://www.nitrc.org/docman/?group_id=1426]]
	58	+ A detailed //VisuAlign //user manual [[can be found here>>https://www.nitrc.org/docman/?group_id=1426]].
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57		-**The basic steps are:**
	60	+**The basic steps are the following:**
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59		--Use the same folder as //QuickNII// with your png images and series descriptor (XML file). You will need the JSON version of the descriptor (it is generated by //QuickNII// by clicking “Save JSON”).
	62	+1. Export your anchoring results from QuickNII in JSON format (click “Save JSON” in the Manage Data window). Save the file in the same folder as your image series.
	63	+1. Open VisuAlign by double-clicking on “VisuAlign.bat”, and load your image descriptor JSON (File -> Open).
	64	+1. Add markers for adjusting the non-linear alignment. Drag a marker to move the atlas borders around it. Start with the borders of the section, and then adjust internal landmarks to fine-tune the alignment between the section and the atlas. Keep the number of markers to a minimum.
	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	+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	+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.
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61		--Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by //QuickNII//.
	70	+== (% style="color:#c0392b" %)**Examples of use**(%%) ==
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63		--Add markers and drag them to move the atlas borders. Start with the borders of the tissue and then adjust internal landmarks.
	72	+(% style="color:#c0392b" %)**Visit the QuickNII and VisuAlign collab**
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65		-NB: keep the number of markers to a minimum.
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67		--The outline mode is toggled by pulling the opacity slider to the far right (as seen in the screenshot). A color picker to the right of it becomes active for changing outline colour.
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69		--“Debug mode” displays triangles representing the deformation field, it is enabled from the View menu (and also enables a colour picker for changing the colour of the triangles).
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71		-- Use the “Save As”  to save your deformations as a new JSON file.
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