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1		-XWiki.sharoncy
	1	+XWiki.puchades

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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>>doc:Collabs.quint.1\. Preparing the images.WebHome]] 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
34		-**The basic steps are:**
	28	+(% class="box infomessage" %)
	29	+(((
	30	+The alignment procedure consists of two main tasks:
35	35
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..)
	32	+1. Determine the dorsoventral and mediolateral cutting angle of the section series, apply same angles for all slices.
	33	+1. Adjust the atlas slices generated along these angles to match individual sections.
	34	+)))
37	37
38		--Use the** transparency slider** continuously to determine how well the atlas fits the section. Determine the sectioning angles (dorso-ventral and medio-lateral) by tilting the atlas and adjust the atlas borders.
	36	+=== (% style="color:#c0392b" %)A) To determine the cutting angles:(%%) ===
39	39
40		--Save the positions for this section for now, they can be adjust later.
	38	+1. Open an image in the beginning of the series, and use anatomical landmarks to find the approximate anteroposterior position of the section in the atlas. Select the atlas modality to be overlaid on the image (MRI, Atlas, etc.)
	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	+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	+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. Ideally, the cutting angles should be consistent throughout the entire section series.
	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.
41	41
42		--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 the positions.
	45	+=== (% style="color:#c0392b" %)B) To fine-tune your alignment:(%%) ===
43	43
44		--Explore a few sections in order to find the angles that fit most sections in order to achieve a global anchoring.
	47	+Review the position of **all sections** in the series, adjust the width and height of atlas slices as necessary, **and save settings**.
45	45
	49	+
46	46	-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.
47	47
48	48	-Review the atlas to section match for all the sections, adjusting the atlas borders as necessary, and save.
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53	53
54	54	**[[image:VisuAlign_illustration.png]]**
55	55
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]]
	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]]
57	57
58	58	**The basic steps are:**
59	59
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”).
	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”).
61	61
62		--Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by QuickNII.
	66	+-Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by //QuickNII//.
63	63
64	64	-Add markers and drag them to move the atlas borders. Start with the borders of the tissue and then adjust internal landmarks.
65	65
66	66	NB: keep the number of markers to a minimum.
67	67
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.
	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.
69	69
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).
	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).
71	71
72	72	- Use the “Save As”  to save your deformations as a new JSON file.

BICCN_QNII_figure.jpg

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