Last modified by puchades on 2021/12/07 10:37
From version 15.1
edited by sharoncy
on 2020/03/28 14:06
Change comment: There is no comment for this version
To version 4.1
edited by puchades
on 2020/03/24 09:55
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
Author
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1 -XWiki.sharoncy
1 +XWiki.puchades
Content
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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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3 3  
4 -**The //Transform// feature in the //Nutil// software **enables **image rotation, renaming, resizing and mirroring** and is used to prepare the images in the series for //QuickNII //alignment and //ilastik //segmentation.
4 +**The //Transform// feature in the //Nutil// software **enables **image rotation, renaming, resizing and mirroring** and was used to prepare the image series for //QuickNII //alignment and //ilastik //segmentation.
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6 ->(% 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.
6 +>The input size requirements for the //QuickNII// and //ilastik// software differ. Naming convention of files is important.
7 7  
8 -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.
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 9  
10 -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).
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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12 -=== (% style="color:#c0392b" %)Naming convention(%%) ===
14 +==== **Naming convention:** ====
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14 -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).
16 +For //QuickNII, //the// //serial section images should be assigned consecutive serial numbers, preferably indicated by three-digit numbers at the end of the file name, e.g. Sample_ID_s001.tif. Section sampling is given by the serial numbers.
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16 -Example: tg2345_MMSH_s001_segmentation.png
18 +For running the QUINT analysis the Segmentation files and the customized atlas maps need to match and therefore
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18 -(It is fine to include a string of letters and numbers followed by the unique ID).
20 +=== H3 Headings Will Appear In The Table of Content ===
19 19  
22 +==== You can also add images ====
20 20  
21 -=== (% style="color:#c0392b" %)Running the transformation(%%) ===
24 +[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
22 22  
23 -Consult the Nutil user manual for detailed procedure (lincluded in the Nutil package available for download at Nitrc.org)
26 +Photo by David Clode
24 24  
25 -[[image:Figure_2_v3.jpg]]
28 +==== Or code ====
29 +
30 +Code blocks can be added by using the code macro:
31 +
32 +{{code language="python"}}
33 +x = 1
34 +if x == 1:
35 + # indented four spaces
36 + print("x is 1.")
37 +{{/code}}
38 +
39 +(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
40 +
Figure_2_v3.jpg
Author
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1 -XWiki.puchades
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1 -4.4 MB
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