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1		-== (% style="color:#c0392b" %)Image pre-processing with Nutil Transform(%%) ==
	1	+== Image pre-processing with Nutil Transform ==
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4	4	**The //Transform// feature in the //Nutil// software **enables **image rotation, renaming, resizing and mirroring** and is used to prepare the image series for //QuickNII //alignment and //ilastik //segmentation.
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12	12	For //ilastik// (Borg et al.2019), the resizing was performed in order to enable efficient processing. To clarify, the pixel classification algorithm relies on input from manual user annotations of training images, and the features ‒ intensity, edge and/or texture ‒ of the image pixels.  In practice, a test run was performed with //ilastik// on images of different sizes to find the optimal resolution for segmentation, with a final resize factor of e.g 0.1  for cellular features, and a factor of 0.05 for series with larger features like Alzheimer plaques.
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14		-=== (% style="color:#c0392b" %)Naming convention(%%) ===
	14	+=== Naming convention: ===
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16	16	For running the QUINT analysis the segmentation files and the customized atlas maps need to match and therefore the segmentation files should follow the same naming format.The file name that correspond to a particular section must contain a unique ID in the format: sXXX.., with XXX.. representing the section number. The section number should reflect 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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20	20	(It is fine to include a string of letters and numbers followed by the unique ID).
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23		-=== (% style="color:#c0392b" %)Running the transformation(%%) ===
	23	+=== Running the transformation ===
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25	25	Consult the Nutil user manual for detailed procedure (link to Manual on Nitrc.org)
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