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1	1	== [[image:BICCN_QNII_figure.png]] ==
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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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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]]
	55	+ A detailed //VisuAlign //user manual can be found at [[https:~~/~~/www.nitrc.org/docman/?group_id=1426>>https://www.nitrc.org/docman/?group_id=1426]]
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57		-**The basic steps are:**
	57	+**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”).
60		-
61		--Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by //QuickNII//.
62		-
63		--Add markers and drag them to move the atlas borders. Start with the borders of the tissue and then adjust internal landmarks.
64		-
65		-NB: keep the number of markers to a minimum.
66		-
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.
68		-
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).
70		-
71		-- Use the “Save As”  to save your deformations as a new JSON file.
	59	+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.
	60	+1. Open VisuAlign by double-clicking on “VisuAlign.bat”, and load your image descriptor JSON (File -> Open).
	61	+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.
	62	+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.
	63	+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.
	64	+1. Finally, use File -> Save As to save your fine-tuned alignment as a new JSON file.