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1	1	== [[image:BICCN_QNII_figure.png]] ==
2	2
3		-== (% style="color:#c0392b" %)//QuickNII// and //VisuAlign//(%%) ==
	3	+== ==
4	4
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.
	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:
7	7
8		-(% class="wikigeneratedid" %)
9		-**//VisuAlign//** enables manual adjustments of the //QuickNII// atlas maps by nonlinear transformation to better match the sections.
	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.
10	10
11		-(% class="wikigeneratedid" %)
12		-The** QUINT workflow** is compatible with the atlas map output of both //QuickNII// and //VisuAlign// (the //VisuAlign// step is optional).
	10	+Further steps of the QUINT workflow are compatible with the atlas map output of both QuickNII and VisuAlign (the VisuAlign step is optional).
13	13
14	14	== (% style="color:#c0392b" %)Preparation of the image series(%%) ==
15	15
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.
	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.
17	17
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).
	16	+=== (% style="color:#c0392b" %)Generate your image descriptor file with FileBuilder(%%) ===
19	19
20		-=== (% style="color:#c0392b" %)Generate your images descriptor file with FileBuider(%%) ===
	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.**
21	21
22		-(% 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.**
23		-
24	24	== (% style="color:#c0392b" %)Open //QuickNII// and load your images(%%) ==
25	25
26	26	(% 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	27
28	28	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/]]
29	29
30		->(% style="color:#27ae60" %)The idea is to determine the cutting angles (dorso-ventral and medio-lateral) for the whole series as these should be consistent throughout. Once found in a few sections, apply the same angles to the rest of the series.
31		-
32	32	== (% style="color:#c0392b" %)**Anchoring procedure**(%%) ==
33	33
	28	+(% class="box infomessage" %)
	29	+(((
	30	+(% style="color:#27ae60" %)The idea is to determine the cutting angles (dorso-ventral and medio-lateral) for the whole series as these should be consistent throughout. Once found in a few sections, apply the same angles to the rest of the series.
	31	+)))
	32	+
34	34	**The basic steps are:**
35	35
36	36	(% style="color:#000000" %)-(%%)Open one image in the beginning of the series and use anatomical landmarks to find the approximate anteroposterior position of the section. Select the atlas modality to be overlayed on the image (MRI, Atlas, etc..)