Version 20.1 by puchades on 2020/04/07 16:47
Show last authors
1 == (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
2
3 A detailed user manual is included when downloading the software.
4
5 [[image:Nutil_main.PNG]]
6
7 **Basic steps:**
8
9 **//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat).
10
11 It requires the following input:
12
13 1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
14
15 **Requirement:**
16
17 *
18 ** Input format: 24-bit RGB images in PNG
19 ** 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).
20 ** //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).
21
22 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.
23
24 (% start="2" %)
25 1. (% style="color:#c0392b" %)**Customised atlas maps**
26
27 Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
28
29 (% start="3" %)
30 1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
31
32 [[image:Illustration seg_flat_files.png||height="254" width="500"]]
33
34 == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
35
36
37 The Nutil software is currently compatible with:
38
39 - Allen mouse brain Atlas (CCFv3, 2015 or 2017)
40
41 - Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3.