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Last modified by puchades on 2021/12/07 10:37
From version 4.3
edited by puchades
on 2020/03/24 11:25
Change comment: There is no comment for this version
To version 4.2
edited by puchades
on 2020/03/24 09:56
Change comment: There is no comment for this version

Summary

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1 1  == Image pre-processing with Nutil Transform ==
2 2  
3 3  
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 +**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.
5 5  
6 ->The image input size requirements for the //QuickNII// and //ilastik// software differ. Naming convention of files is important.
6 +>The input size requirements for the //QuickNII// and //ilastik// software differ. Naming convention of files is important.
7 7  
8 8  For //QuickNII,// the input requirements described in (Puchades et al., 2019) are:
9 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
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13 13  
14 14  ==== **Naming convention:** ====
15 15  
16 -The file names of the segmentation and atlas maps 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).
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.
17 17  
18 -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
19 19  
20 -(It is fine to include a string of letters and numbers followed by the unique ID).
21 -
22 -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.
23 -
24 24  === H3 Headings Will Appear In The Table of Content ===
25 25  
26 26  ==== You can also add images ====