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1	1	== [[image:BICCN_QNII_figure.png]] ==
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3		-(% class="wikigeneratedid" id="H-1" %)
4		-(% class="small" %)Section image registration using QuickNII
	3	+== ==
5	5
6		-
7		-
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 on [[https:~~/~~/www.nitrc.org/projects/quicknii/>>https://www.nitrc.org/projects/quicknii/]]
28	28
29	29	== (% style="color:#c0392b" %)**Anchoring procedure**(%%) ==
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56	56	**[[image:VisuAlign_illustration.png]]**
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58		- A detailed //VisuAlign //user manual [[can be found here>>https://www.nitrc.org/docman/?group_id=1426]].
	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]]
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60		-**The basic steps are the following:**
	57	+**The basic steps are:**
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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.
	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”).
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70		-== (% style="color:#c0392b" %)**Examples of use**(%%) ==
	61	+-Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by //QuickNII//.
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72		-(% style="color:#c0392b" %)**Visit the QuickNII and VisuAlign collab**
	63	+-Add markers and drag them to move the atlas borders. Start with the borders of the tissue and then adjust internal landmarks.
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	65	+NB: keep the number of markers to a minimum.
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75		-
	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.