Attention: The EBRAINS drive will be unavailable for most of the weekend starting the 25th October. Although the Lab is availble while the Drive is down, files that are stored in the Drive will not be loaded and you will be unable to save documents directly on the Lab.


Version 32.1 by annedevismes on 2021/06/08 11:56
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_GUI.png||style="float:left"]]
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36 **Basic steps**
37
38 //Nutil Quantifier// quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent-brain section images (mouse or rat).
39
40 It requires the following input.
41
42 1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
43
44 **Requirement**
45
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).
49
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.
51
52 (% start="2" %)
53 1. (% style="color:#c0392b" %)**Customised atlas maps**
54
55 Generate the atlas maps in FLAT format with the //QuickNII //software (or with //VisuAlign//).
56
57 (% start="3" %)
58 1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
59
60 [[image:Illustration seg_flat_files.png]]
61
62 == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
63
64
65 The //Nutil //software is currently compatible with
66
67 * Allen mouse brain Atlas (CCFv3, 2015 or 2017) and
68 * Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3.