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1	1	== [[image:BICCN_QNII_figure.png]] ==
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3	3	(% class="wikigeneratedid" id="H-1" %)
4		-(% class="small" %)Section image registration using QuickNII
	4	+(% class="small" %)Section image registration using //QuickNII//
5	5
6	6
7	7
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:
	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.
9	9
10		-1. QuickNII guides you through an interactive affine alignment, including propagation of alignment settings across the section series.
11		-1. VisuAlign lets you fine-tune your alignment using non-linear adjustments.
	10	+1. //QuickNII //guides you through an interactive affine alignment, including propagation of alignment settings across the section series.
	11	+1. //VisuAlign //allows you to fine-tune your alignment by using non-linear adjustments.
12	12
13		-Further steps of the QUINT workflow are compatible with the atlas map output of both QuickNII and VisuAlign (the VisuAlign step is optional).
	13	+Further steps of the //QUINT// workflow are compatible with the atlas map output of both //QuickNII //and //VisuAlign //(the //VisuAlign //step is optional).
14	14
15	15	== (% style="color:#c0392b" %)Preparation of the image series(%%) ==
16	16
17		-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	+Before you get started with image registration, make sure your images have 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.
18	18
19	19	=== (% style="color:#c0392b" %)Generate your image descriptor file with FileBuilder(%%) ===
20	20
21		-(% 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	+(% 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 resised images.**
22	22
23	23	== (% style="color:#c0392b" %)Open //QuickNII// and load your images(%%) ==
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31	31	(% class="box infomessage" %)
32	32	(((
33		-The alignment procedure consists of two main tasks:
	33	+The alignment procedure consists of two main tasks.
34	34
35		-1. Determine the dorsoventral and mediolateral cutting angle of the section series, apply same angles for all slices.
	35	+1. Determine the dorsoventral and mediolateral cutting angle of the section series and apply the same angles for all slices.
36	36	1. Adjust the atlas slices generated along these angles to match individual sections.
37	37	)))
38	38
39		-=== (% style="color:#c0392b" %)A) To determine the cutting angles:(%%) ===
	39	+=== (% style="color:#c0392b" %)A. Determine the cutting angles(%%) ===
40	40
41		-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.)
	41	+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.).
42	42	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.
43	43	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.
44		-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.
45		-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.
46		-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.
	44	+1. Open another image, located at the **other end of the series**, and repeat the same procedure as above:, that is, find the approximate anteroposterior position of the section and test how well the cutting angles fit this section. Save your settings.
	45	+1. Explore a few sections throughout the series to 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.
	46	+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 on the basis of the section numbering.
47	47
48		-=== (% style="color:#c0392b" %)B) To fine-tune your alignment:(%%) ===
	48	+=== (% style="color:#c0392b" %)B. Fine-tune your alignment(%%) ===
49	49
50		-Review the position of **all sections** in the series, adjust the width and height of atlas slices as necessary, **and save settings**.
	50	+Review the position of **all sections** in the series, adjust the width and height of the atlas slices as necessary, **and save the settings**.
51	51
52		-**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.
	52	+**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 performed by using //Nutil //Quantifier.
53	53
54		-== (% style="color:#c0392b" %)**Nonlinear adjustment with VisuAlign**(%%) ==
	54	+== (% style="color:#c0392b" %)**Non-linear adjustment with //VisuAlign//**(%%) ==
55	55
56	56	**[[image:VisuAlign_illustration.png]]**
57	57
58	58	A detailed //VisuAlign //user manual [[can be found here>>https://www.nitrc.org/docman/?group_id=1426]].
59	59
60		-**The basic steps are the following:**
	60	+**The basic steps are as follows.**
61	61
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.
	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 to change 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	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.
	68	+1. There is also an “Export” function for generating .flat files for **Nutil**.
69	69
70	70	== (% style="color:#c0392b" %)**Examples of use**(%%) ==
71	71