Last modified by puchades on 2021/11/16 09:11

From version 31.1
edited by puchades
on 2020/09/24 13:05
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To version 7.1
edited by puchades
on 2020/03/26 10:53
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1 1  == (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
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3 -A detailed user manual is included when downloading the software.
3 +A detailed Nutil user manual is included when downloading the software.
4 4  
5 -[[image:Nutil_GUI.png||style="float:left"]]
5 +[[image:Quantifier.PNG]]
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36 36  **Basic steps:**
37 37  
38 -**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat).
9 +**//Quantifier//** locates and quantifies labeling identified by segmentation in rodent brain section images (mouse or rat).
39 39  
40 40  It requires the following input:
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42 -1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
13 +1. (% style="color:#c0392b" %)**Segmentations with the labeling displayed in one RGB colour**
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44 44  **Requirement:**
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46 -* Input format: 24-bit RGB images in PNG
47 -* The images have to have the same aspect ratio as the images used in QuickNII to generate the atlas maps (can be a different size).
48 -* //Quantifier** **//is only able to extract one RGB colour at a time. Apply one RBG colour to all of the objects of interest, and specify this colour co//d//e in the GUI (e.g. 255, 0, 0 for red).
17 +* must be 24-bit RGB images in PNG format
18 +* same proportions as the images used in QuickNII to generate the atlas maps (can be a different size)
19 +* //Quantifier** **//is only able to extract one RGB colour at a time. Apply one RBG colour to all of the objects of interest, and specify this colour code in the //Excel template//.
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50 50  To generate the segmentations we recommend the //Pixel and// //Object Classification workflows// in the //ilastik// software (//ilastik.org//). However, any image analysis software may be used.
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52 52  (% start="2" %)
53 -1. (% style="color:#c0392b" %)**Customised atlas maps**
24 +1. (% style="color:#c0392b" %)**Customised anatomical atlas maps**
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55 -Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
26 +Generate the atlas maps in FLAT format with the //QuickNII //software
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58 58  1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
30 +1. (% style="color:#c0392b" %)**Reference atlas label file**(%%) (in LABEL format) corresponding to the relevant atlas. The following reference atlases are included in the //Nutil// package (in the “Labels” folder). 
59 59  
60 -[[image:Illustration seg_flat_files.png]]
32 +[[image:Illustration seg_flat_files.png||height="254" width="500"]]
61 61  
62 -== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
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65 -The Nutil software is currently compatible with:
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67 -* Allen mouse brain Atlas (CCFv3, 2015 or 2017)
68 -* Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3. 
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