Last modified by puchades on 2021/12/07 10:37
From version 11.1
edited by puchades
on 2020/03/26 10:47
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To version 16.1
edited by puchades
on 2020/04/07 15:50
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Summary

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Title
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1 -2. Image preparation with Nutil Transform
1 +2. Image pre-processing with Nutil Transform
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1 -== (% style="color:#c0392b" %)Image pre-processing with Nutil Transform(%%) ==
1 +**The //Transform// feature in the //Nutil// software **enables **image rotation, renaming, resizing and mirroring,** and is used to prepare image series for atlas alignment with QuickNII and segmentation with ilastik. It should be noted that QuickNII and ilastik have different input image size requirements. In addition, it is important that the input images follow the standard naming convention described below..
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3 +>(% style="color:#27ae60" %)The //QuickNII// and //ilastik// software have different input image size requirements. It is also important that the input images follow the prescribed naming convention.
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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.
5 +== (% style="color:#c0392b" %)Input requirements(%%) ==
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6 ->(% style="color:#27ae60" %)The image input size requirements for the //QuickNII// and //ilastik// software differ. Naming convention of files is important.
7 +For //QuickNII,// the input requirements are described in in Puchades et al., 2019. To summarise, images should be in 24-bit PNG or JPEG format, and can be loaded up to a 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. For a standard FullHD or WUXGA display (1920x1080 or 1920x1200 pixels) the useful image area is approximately 1500x1000 pixels. Using a similar resolution ensures optimal image-loading performance.
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8 -For //QuickNII,// the input requirements described in (Puchades et al., 2019) are:
9 -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. For a standard FullHD or WUXGA display
10 -(1920x1080 or 1920x1200 pixels) the useful image area is approximately 1500x1000 pixels,using a similar resolution ensures optimal image-loading performance.
9 +For //ilastik// (Borg et al.2019) images are downscaled in order to enable efficient processing. The pixel classification algorithm relies on input from manual user annotations of the training images, and the features ‒ intensity, edge and/or texture ‒ of the image pixels. The resizing factor is determined by trial and error, with a test run performed with //ilastik// on images of different sizes to determine the optimal resolution for segmentation. As an example, in Yates et al., 2019, the images were downscaled by a factor of 0.1 and 0.05 for cellular features and Alzheimer's plaques respectively (factor applies to the image width here).
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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 14  === (% style="color:#c0392b" %)Naming convention(%%) ===
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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).
13 +For QUINT analysis, Nutil Quantifier quantifies objects extracted from segmentations and registers them to regions defined by customised atlas maps. To match segmentations and corresponding atlas maps together, Nutil Quantifier relies on a unique ID in the file name of both files.The ID should be unique to the particular brain section and 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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18 18  Example: tg2345_MMSH_s001_segmentation.png
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23 23  === (% style="color:#c0392b" %)Running the transformation(%%) ===
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25 -Consult the Nutil user manual for detailed procedure (link to Manual on Nitrc.org)
22 +Consult the Nutil user manual for detailed procedure (lincluded in the Nutil package available for download at Nitrc.org)
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27 27  [[image:Figure_2_v3.jpg]]