Last modified by puchades on 2021/12/07 10:37
From version 16.2
edited by puchades
on 2020/04/07 15:51
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To version 12.1
edited by sharoncy
on 2020/03/28 13:58
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Title
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1 -2. Image pre-processing with Nutil Transform
1 +2. Image preparation with Nutil Transform
Author
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1 -XWiki.puchades
1 +XWiki.sharoncy
Content
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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..
1 +== (% style="color:#c0392b" %)Image pre-processing with Nutil Transform(%%) ==
2 2  
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.
4 4  
5 -== (% style="color:#c0392b" %)Input requirements(%%) ==
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.
6 6  
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.
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.
8 8  
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).
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.
10 10  
11 -== (% style="color:#c0392b" %)Naming convention(%%) ==
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).
12 12  
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).
14 +=== (% style="color:#c0392b" %)Naming convention(%%) ===
14 14  
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).
17 +
15 15  Example: tg2345_MMSH_s001_segmentation.png
16 16  
17 17  (It is fine to include a string of letters and numbers followed by the unique ID).
18 18  
19 19  
20 -== (% style="color:#c0392b" %)Running the transformation(%%) ==
23 +=== (% style="color:#c0392b" %)Running the transformation(%%) ===
21 21  
22 -Consult the Nutil user manual for detailed procedure (lincluded in the Nutil package available for download at Nitrc.org)
25 +Consult the Nutil user manual for detailed procedure (link to Manual on Nitrc.org)
23 23  
24 24  [[image:Figure_2_v3.jpg]]