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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 12.1
edited by sharoncy
on 2020/03/28 13:58
Change comment: There is no comment for this version

Summary

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Title
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1 -1. Image preparation with Nutil
1 +2. Image preparation with Nutil Transform
Content
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1 -== H2 Headings Will Appear in Table of Content ==
1 +== (% style="color:#c0392b" %)Image pre-processing with Nutil Transform(%%) ==
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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.
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.
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6 ->This is a quote. You can add a quote by selecting some text and clicking the quote button in the editor.
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.
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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.
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 -=== H3 Headings Will Appear In The Table of Content ===
12 +For //ilastik// (Borg et al.2019) the histological 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 image were downscaled by a factor of 0.1 and 0.05 for cellular features and Alzheimer's plaques respectively (factor applies to image width).
11 11  
12 -==== You can also add images ====
14 +=== (% style="color:#c0392b" %)Naming convention(%%) ===
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14 -[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
16 +For QUINT analysis, Nutil Quantifier extracts objects from segmentations and registers them to areas defined in 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 is unique to a particular section and should be 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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16 -Photo by David Clode
18 +Example: tg2345_MMSH_s001_segmentation.png
17 17  
18 -==== Or code ====
20 +(It is fine to include a string of letters and numbers followed by the unique ID).
19 19  
20 -Code blocks can be added by using the code macro:
21 21  
22 -{{code language="python"}}
23 -x = 1
24 -if x == 1:
25 - # indented four spaces
26 - print("x is 1.")
27 -{{/code}}
23 +=== (% style="color:#c0392b" %)Running the transformation(%%) ===
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29 -(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
30 -
25 +Consult the Nutil user manual for detailed procedure (link to Manual on Nitrc.org)
26 +
27 +[[image:Figure_2_v3.jpg]]
Figure_2_v3.jpg
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1 +XWiki.puchades
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1 +4.4 MB
Content