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Last modified by puchades on 2022/02/18 13:55
From version 29.1
edited by puchades
on 2020/09/23 13:44
Change comment: There is no comment for this version
To version 13.1
edited by sharoncy
on 2020/03/26 19:21
Change comment: There is no comment for this version

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1 +XWiki.sharoncy
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1 1  == [[image:BICCN_QNII_figure.png]] ==
2 2  
3 -(% class="wikigeneratedid" id="H-1" %)
4 -Image registration using QuickNII
3 +== (% style="color:#c0392b" %)Preparation of the image series(%%) ==
5 5  
5 +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.
6 6  
7 +(% 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).
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:
9 +=== (% style="color:#c0392b" %)Generate your images descriptor file with FileBuider(%%) ===
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.
11 +(% 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.**
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 +== (% style="color:#c0392b" %)Open QuickNII and load your images(%%) ==
14 14  
15 -== (% style="color:#c0392b" %)Preparation of the image series(%%) ==
15 +(% 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.
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 +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/]]
18 18  
19 -=== (% style="color:#c0392b" %)Generate your image descriptor file with FileBuilder(%%) ===
19 +>(% style="color:#27ae60" %)The idea is to determine the cutting angles (dorso-ventral and medio-lateral) for the whole serie as these should be consistent. Once found in a few sections, apply the same angles to the rest of the serie.
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:#c0392b" %)**Anchoring procedure**(%%) ==
22 22  
23 -== (% style="color:#c0392b" %)Open //QuickNII// and load your images(%%) ==
23 +**The basic steps are:**
24 24  
25 -(% 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.
25 +(% 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 to the image (MRI, Atlas, etc..)
26 26  
27 -A detailed //QuickNII// user manual as well as a demo dataset [[can be found here>>https://www.nitrc.org/docman/?group_id=1341]].
27 +-**The transparency slider** can be used 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.
28 28  
29 -== (% style="color:#c0392b" %)**Anchoring procedure**(%%) ==
29 +-Save the positions for this section for now, you can adjust these later.
30 30  
31 -(% class="box infomessage" %)
32 -(((
33 -The alignment procedure consists of two main tasks:
31 +-Open the next image, located at the other end of the serie 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.
34 34  
35 -1. Determine the dorsoventral and mediolateral cutting angle of the section series, apply same angles for all slices.
36 -1. Adjust the atlas slices generated along these angles to match individual sections.
37 -)))
33 +-Explore a few sections in order to find the angles fitting most sections in order to achieve a global anchoring.
38 38  
39 -=== (% style="color:#c0392b" %)A) To determine the cutting angles:(%%) ===
35 +-By having the same angles in these two sections (i.e. ML=+1; DV= -4), QuickNII will apply them to all other sections located in between. The antero-posterior positions of all images are also estimated.
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.)
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 -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.
37 +-Review all sections, adjust atlas borders and save.
47 47  
48 -=== (% style="color:#c0392b" %)B) To fine-tune your alignment:(%%) ===
39 +-Export custom atlas slices corresponding to your series by clicking on the **“export Slices”** button. The exported .flat files are used for the quantification by Nutil Quantifier.
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**.
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.
53 -
54 54  == (% style="color:#c0392b" %)**Nonlinear adjustment with VisuAlign**(%%) ==
55 55  
56 56  **[[image:VisuAlign_illustration.png]]**
57 57  
58 - A detailed //VisuAlign //user manual [[can be found here>>https://www.nitrc.org/docman/?group_id=1426]].
45 +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]]
59 59  
60 -**The basic steps are the following:**
47 +**The basic steps are:**
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.
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.
49 +-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”).
50 +
51 +-Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by QuickNII.
52 +
53 +-Add markers and drag them to move the atlas borders. Start with the borders of the tissue and then adjust internal landmarks.
54 +
55 +NB: keep the number of markers to a minimum.
56 +
57 +-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.
58 +
59 +-“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).
60 +
61 +- Use the “Save As”  to save your deformations as a new JSON file.
BICCN_QNII_figure.jpg
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