Last modified by puchades on 2021/11/16 09:11
From version 5.2
edited by puchades
on 2020/03/25 17:05
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To version 31.2
edited by annedevismes
on 2021/06/08 11:01
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1 -== Nutil Quantifier ==
1 +== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
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3 -A detailed Nutil user manual is included when downloading the software.
3 +A detailed user manual is included when downloading the software.
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5 -[[image:Quantifier.PNG]]
5 +[[image:Nutil_GUI.png||style="float:left"]]
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7 -**Basic steps:**
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9 -**//Quantifier//** locates and quantifies labelling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:
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12 -1. **Segmentations with the labeling displayed in one RGB colour**
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14 -**Requirement:**
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16 -* must be 24-bit RGB images in PNG format
17 -* same proportions as the images used in QuickNII to generate the atlas maps (can be a different size)
18 -* //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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20 -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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35 +
36 +**Basic steps**
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38 +//Nutil Quantifier// quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent-brain section images (mouse or rat).
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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**
43 +
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 code in the GUI (e.g., 255, 0, 0 for red).
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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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23 -1. **Customised anatomical atlas maps**
53 +1. (% style="color:#c0392b" %)**Customised atlas maps**
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25 -Generate the atlas maps in FLAT format with the //QuickNII //software
55 +Generate the atlas maps in FLAT format with the //QuickNII //software (or with //VisuAlign//).
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28 -1. **Anchored XML** file generated with the //QuickNII// software.
29 -1. **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). 
58 +1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
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31 -[[image:Illustration seg_flat_files.png||height="254" width="500"]]
60 +[[image:Illustration seg_flat_files.png]]
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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) and
68 +* Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3. 
Quantifier.PNG
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Nutil_main.PNG
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