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1	1	== [[image:BICCN_QNII_figure.png]] ==
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3		-== Preparation of the image serie ==
	3	+== (% style="color:#c0392b" %)Preparation of the image serie(%%) ==
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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.
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7	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).
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9		-=== (% style="color:#000000" %)Generate your images descriptor file with FileBuider(%%) ===
	9	+=== (% style="color:#c0392b" %)Generate your images descriptor file with FileBuider(%%) ===
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11	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.**
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13		-== Open QuickNII and load your images ==
	13	+== (% style="color:#c0392b" %)Open QuickNII and load your images(%%) ==
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15	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.
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19	19	>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.
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21		-== **Anchoring procedure** ==
	21	+== (% style="color:#c0392b" %)**Anchoring procedure**(%%) ==
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23	23	**The basic steps are:**
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39	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.
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41		-== **Nonlinear adjustment with VisuAlign** ==
	41	+== (% style="color:#c0392b" %)**Nonlinear adjustment with VisuAlign**(%%) ==
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43	43	**[[image:VisuAlign_illustration.png]]**
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