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1	1	== [[image:BICCN_QNII_figure.png]] ==
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3		-== ==
	3	+== ==
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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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39	39	1. **Tilt the atlas** by adjusting the dorsoventral and mediolateral angles. **Move the transparency slider** back and forth to see how well the atlas fits the section. The size of the atlas slice can also be modified for a better fit.
40	40	1. Once you have a fairly good match, save the alignment settings for this section and move on with the anchoring procedure. The settings can be fine-tuned later.
41	41	1. Open another image, located at the **other end of the series**, and repeat the same procedure as above:, i.e. find the approximate anteroposterior position of the section, and test how well the cutting angles fit this section. Save your settings.
42		-1. Explore a few sections throughout the series in order to and find the angles that fit most sections in order to achieve a **good global anchoring**. We recommend to keep the cutting angles consistent throughout the entire section series, unless two blocks were cut separately.
	42	+1. Explore a few sections throughout the series in order to and find the angles that fit most sections in order to achieve a **good global anchoring**. We recommend to keep the cutting angles consistent throughout the entire section series (i.e. ML=+1; DV= -4), unless two blocks were cut separately.
43	43	1. Once two or more sections are anchored at their approximate position within the brain, **QuickNII propagates** **the cutting angles** across the entire image series. The anteroposterior position of the images is also estimated based on the section numbering.
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45	45	=== (% style="color:#c0392b" %)B) To fine-tune your alignment:(%%) ===
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47	47	Review the position of **all sections** in the series, adjust the width and height of atlas slices as necessary, **and save settings**.
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	49	+**Done! **Now you can **export customised atlas maps** corresponding to your series by clicking on the “Export Slices” button. The exported .flat files are used for the quantification by using Nutil Quantifier.
49	49
50		--By having the same cutting angles set for two sections (i.e. ML=+1; DV= -4), //QuickNII// will apply them to all the sections located between them. The antero-posterior positions of all the images are also estimated based on the numbering.
51		-
52		--Review the atlas to section match for all the sections, adjusting the atlas borders as necessary, and save.
53		-
54		--Export customised atlas maps corresponding to your series by clicking on the **“export Slices”** button. The exported .flat files are used for the quantification by //Nutil Quantifier//.
55		-
56	56	== (% style="color:#c0392b" %)**Nonlinear adjustment with VisuAlign**(%%) ==
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58	58	**[[image:VisuAlign_illustration.png]]**
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60		- 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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62		-**The basic steps are:**
	57	+**The basic steps are the following:**
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64		--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”).
65		-
66		--Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by //QuickNII//.
67		-
68		--Add markers and drag them to move the atlas borders. Start with the borders of the tissue and then adjust internal landmarks.
69		-
70		-NB: keep the number of markers to a minimum.
71		-
72		--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.
73		-
74		--“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).
75		-
76		-- 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.