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  • BICCN_QNII_figure.jpg

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1	1	== [[image:BICCN_QNII_figure.png]] ==
2	2
3		-== ==
	3	+== (% style="color:#c0392b" %)//QuickNII// and //VisuAlign//(%%) ==
4	4
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:
	5	+(% class="wikigeneratedid" %)
	6	+**//QuickNII//** enable the registeration of the brain section images to the reference atlas to generate atlas maps that are customised to match the cutting plane and proportions of the sections. The adjusted are done by linear transformation only to allow angles to be calculated.
6	6
7		-1. QuickNII guides you through an interactive affine alignment, including propagation of alignment settings across the section series.
8		-1. VisuAlign lets you fine-tune your alignment using non-linear adjustments.
	8	+(% class="wikigeneratedid" %)
	9	+**//VisuAlign//** enables manual adjustments of the //QuickNII// atlas maps by nonlinear transformation to better match the sections.
9	9
10		-Further steps of the QUINT workflow are compatible with the atlas map output of both QuickNII and VisuAlign (the VisuAlign step is optional).
	11	+(% class="wikigeneratedid" %)
	12	+**The QUINT workflow** is compatible with atlas map output of //QuickNII// and //VisuAlign// (the //VisuAlign// step is optional).
11	11
12	12	== (% style="color:#c0392b" %)Preparation of the image series(%%) ==
13	13
14		-Before you get started with image registration, make sure your images are the right size, and files are named according to the QUINT naming convention. See [[2. Image pre-processing with Nutil Transform>>2. Image pre-processing with Nutil Transform]] for details.
	16	+Resize your raw 2D images to 24-bit PNG and JPEG. Images can be loaded up to the resolution of 16 megapixels (e.g.4000x4000 or 5000x3000 pixels), however QuickNII does not benefit from image resolutions exceeding the resolution of the monitor in use.
15	15
	18	+(% style="color:#4e5f70" %)The resized files must follow the naming convention having an unique ID in the format: sXXX.., with XXX.. reflecting the serial order and spacing of the sections (e.g. s002, s006, s010 for every 4^^th^^ section starting with section 2).
	19	+
16	16	=== (% style="color:#c0392b" %)Generate your images descriptor file with FileBuider(%%) ===
17	17
18	18	(% style="color:#4e5f70" %)Use the small program “FileBuilder.bat” provided with //QuickNII//. A new window will open, and ask for the folder where your images are located. Point to the correct folder, mark all image files, and click ok. **An XML file is generated**. **Always save this file in the same folder as the resized images.**
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49	49
50	50	**[[image:VisuAlign_illustration.png]]**
51	51
52		- 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]]
	56	+ 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]]
53	53
54	54	**The basic steps are:**
55	55
56		--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	+-Use 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 in QuickNII by clicking “Save JSON”).
57	57
58		--Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by //QuickNII//.
	62	+-Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by QuickNII.
59	59
60	60	-Add markers and drag them to move the atlas borders. Start with the borders of the tissue and then adjust internal landmarks.
61	61
62	62	NB: keep the number of markers to a minimum.
63	63
64		--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	+-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 color.
65	65
66		--“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	+-“Debug mode” displays triangles representing the deformation field, it is enabled from the View menu (and also enables a color picker for changing the color of the triangles).
67	67
68	68	- Use the “Save As”  to save your deformations as a new JSON file.

BICCN_QNII_figure.jpg

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