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Last modified by puchades on 2021/12/07 10:37
From version 2.1
edited by sharoncy
on 2020/03/09 13:50
Change comment: There is no comment for this version
To version 19.2
edited by annedevismes
on 2021/06/08 10:40
Change comment: There is no comment for this version

Summary

Details

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Title
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1 -1. Image preparation with Nutil
1 +2. Image pre-processing with Nutil Transform
Author
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1 -XWiki.sharoncy
1 +XWiki.annedevismes
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1 -== H2 Headings Will Appear in Table of Content ==
1 +**The //Transform// feature in the //Nutil// software **enables **image rotation, renaming, resising, 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.
3 3  
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.
5 +== (% style="color:#c0392b" %)Input requirements(%%) ==
5 5  
6 ->This is a quote. You can add a quote by selecting some text and clicking the quote button in the editor.
7 +For //QuickNII,// the input requirements are described in details in Puchades et al., 2019. To summarise, images should be in 24-bit PNG or JPEG format, with a resolution up to 16 megapixels (e.g., 4000x4000 or 5000x3000 pixels). Keep in mind that //QuickNII //does not benefit from image resolutions exceeding the resolution of the monitor in use. For a standard FullHD or widescreen display (1920x1080 or 1920x1200 pixels), the useful image area in //QuickNII //is approximately 1500x1000 pixels. Using a similar resolution ensures optimal image-loading performance.
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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.
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 resising 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 10 for cellular features and by a factor of 20 for Alzheimer's plaques with respect to image width.
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10 -=== H3 Headings Will Appear In The Table of Content ===
11 +== (% style="color:#c0392b" %)Naming convention(%%) ==
11 11  
12 -==== You can also add images ====
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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14 -[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
15 +Example: tg2345_MMSH_s001_segmentation.png
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16 -Photo by David Clode
17 +It is fine to include a string of letters and numbers followed by the unique ID.
17 17  
18 -==== Or code ====
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20 -Code blocks can be added by using the code macro:
20 +== (% style="color:#c0392b" %)Running the transformation(%%) ==
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22 -{{code language="python"}}
23 -x = 1
24 -if x == 1:
25 - # indented four spaces
26 - print("x is 1.")
27 -{{/code}}
22 +Consult the //Nutil //user manual for the detailed procedure (included in the //Nutil //package [[available for download here>>https://www.nitrc.org/projects/nutil/]]).
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29 -(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
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24 +[[image:Figure_2_v3.jpg]]
Figure_2_v3.jpg
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1 +XWiki.puchades
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1 +4.4 MB
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