Last modified by puchades on 2021/12/07 10:37
From version 11.1
edited by puchades
on 2020/03/26 10:47
Change comment: There is no comment for this version
To version 3.2
edited by puchades
on 2020/03/12 17:44
Change comment: There is no comment for this version

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Title
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1 -2. Image preparation with Nutil Transform
1 +1. Image preparation with Nutil
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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 -**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.
4 +Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
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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.
6 +>This is a quote. You can add a quote by selecting some text and clicking the quote button in the editor.
7 7  
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.
8 +Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
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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.
10 +=== H3 Headings Will Appear In The Table of Content ===
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14 -=== (% style="color:#c0392b" %)Naming convention(%%) ===
12 +==== You can also add images ====
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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).
14 +[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
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18 -Example: tg2345_MMSH_s001_segmentation.png
16 +Photo by David Clode
19 19  
20 -(It is fine to include a string of letters and numbers followed by the unique ID).
18 +==== Or code ====
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20 +Code blocks can be added by using the code macro:
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23 -=== (% style="color:#c0392b" %)Running the transformation(%%) ===
22 +{{code language="python"}}
23 +x = 1
24 +if x == 1:
25 + # indented four spaces
26 + print("x is 1.")
27 +{{/code}}
24 24  
25 -Consult the Nutil user manual for detailed procedure (link to Manual on Nitrc.org)
26 -
27 -[[image:Figure_2_v3.jpg]]
29 +(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
30 +
Figure_2_v3.jpg
Author
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1 -XWiki.puchades
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1 -4.4 MB
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