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Last modified by puchades on 2022/11/02 10:16
From version 68.1
edited by sharoncy
on 2021/10/18 09:46
Change comment: There is no comment for this version
To version 36.1
edited by sharoncy
on 2020/03/30 17:18
Change comment: There is no comment for this version

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2 -(((
3 -==== QUINT software documentation ====
1 +(% style="text-align:center" %)
2 +[[image:QUINT_workflow_pic.png||height="394" width="1011"]]
4 4  
5 -[[QuickNII user documentation>>https://quicknii.readthedocs.io/en/latest/index.html]]
4 +== (% style="color:#c0392b" %)**Workflow Description**(%%) ==
6 6  
7 -[[VisuAlign user documentation>>https://visualign.readthedocs.io/en/latest/index.html]]
6 +The QUINT workflow enables the quantification and spatial analysis of labelled features in histological images of rodent brain sections based on reference atlases of the brain. It utilises three open-source software:
8 8  
9 -[[Ilastik user documentation>>https://nutil.readthedocs.io/en/latest/Ilastik.html]]
8 +1. [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells by segmentation.
9 +1. [[(% style="color:#2980b9" %)//QuickNII//>>doc:.Image registration to reference atlas using QuickNII.WebHome]](%%) generates atlas maps customised to match the proportions and cutting plane of the brain sections. //[[(% style="color:#3498db" %)VisuAlign>>doc:.Image registration to reference atlas using QuickNII.WebHome]]//(%%) enables nonlinear adjustments of the reference atlas to the experimental section.
10 +1. (% style="color:#2980b9" %)//Nutil//(%%) enables image [[transformations>>doc:.1\. Preparing the images.WebHome]], in addition to [[quantification and spatial analysis>>doc:.4\. Quantification and spatial analysis with Nutil.WebHome]] of features by drawing on the output of //ilastik// and //QuickNII//.
10 10  
11 -[[Nutil user documentation>>https://nutil.readthedocs.io/en/latest/index.html]]                                                                   
12 -)))
12 +In combination, the tools facilitate semi-automated quantification, eliminating the need for more time consuming methods such as stereological analysis with manual delineation of brain regions.
13 13  
14 +[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
14 14  
15 -[[image:QUINT_workflow_Plaques.png||height="470" style="float:left" width="1277"]]
16 16  
17 -== ==
18 18  
19 -== ==
20 20  
21 -== ==
22 22  
23 -== ==
24 24  
25 -== ==
26 26  
27 -== ==
28 28  
29 -== (% style="color:#c0392b" %)**Description**(%%) ==
30 30  
31 -**The QUINT workflow enables an atlas-based analysis of extracted features from histological image sections from the rodent brain by using 3D reference atlases. **
32 32  
33 -**Examples of use are cell counting and spatial distributions, determination of projection areas in connectivity experiments, and exploration of pathological hallmarks in brain-disease models. Integration of various data to the same reference space enables new exploration strategies and reuse of experimental data.**
25 +==== ====
34 34  
35 -The workflow is built on the following open-access software.
36 36  
37 -* [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells, by using machine-learning image segmentation.
38 -* [[(% style="color:#2980b9" %)//QuickNII//>>doc:.Image registration to reference atlas using QuickNII.WebHome]](%%) generates custom-angle slices from volumetric brain atlases to match the proportions and cutting plane of histological sections.
39 -* //[[(% style="color:#3498db" %)VisuAlign>>doc:.Image registration to reference atlas using QuickNII.WebHome]]//(%%) is then used for non-linear alignment of the reference-atlas slice to the section image.
40 -* (% style="color:#2980b9" %)//Nutil//(%%) enables image [[transformations>>doc:.1\. Preparing the images.WebHome]], in addition to [[quantification and spatial analysis>>doc:.4\. Quantification and spatial analysis with Nutil.WebHome]] of features by drawing on the output of //ilastik// and //QuickNII//.
41 41  
42 -In combination, the tools facilitate semi-automated quantification, eliminating the need for more time-consuming methods such as stereological analysis with manual delineation of brain regions.
43 43  
44 -[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
45 45  
31 +==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
46 46  
33 +* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
47 47  
35 +(((
36 +* As the quantifications are performed in regions defined by a reference atlas, the region definitions are standardized, allowing comparisons of data from different laboratories.
48 48  
38 +==== (% style="color:#c0392b" %)**References**(%%) ====
49 49  
40 +Yates SC et al. 2019. QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front. Neuroinform. 13:75. doi: 10.3389/fninf.2019.00075
50 50  
42 +[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
51 51  
44 +[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
52 52  
53 -
54 -
55 -
56 -
57 -
58 -
59 -
60 -QUINT workflow video
61 -
62 -== (% style="color:#c0392b" %)**Workflow highlights**(%%) ==
63 -
64 -(% class="box successmessage" %)
65 -(((
66 -The semi-automated QUINT workflow uses open-access software that can be operated without any scripting knowledge.
46 +[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
67 67  )))
68 -
69 -(((
70 -(% class="box successmessage" %)
71 -(((
72 -Because the quantifications are performed in regions defined by a reference atlas, the region definitions are standardised, allowing comparisons of data from different laboratories.
73 -)))
74 -
75 -==== (% style="color:#c0392b" %)**References**(%%) ====
76 -
77 -* Yates SC et al. (2019) QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front. Neuroinform. 13:75. doi: [[10.3389/fninf.2019.00075>>https://www.frontiersin.org/articles/10.3389/fninf.2019.00075/full]]
78 -* Groeneboom NE, Yates SC, Puchades MA and Bjaalie JG (2020) Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. //Front. Neuroinform.// 14:37. doi: [[10.3389/fninf.2020.00037>>https://www.frontiersin.org/articles/10.3389/fninf.2020.00037/full]]
79 -* Berg S, Kutra D, Kroeger T, et al. & Kreshuk A (2019) ilastik: interactive machine learning for (bio)image analysis. Nat Methods. 16:1226-1232. doi: [[10.1038/s41592-019-0582-9>>https://www.nature.com/articles/s41592-019-0582-9]]
80 -* (((
81 -Puchades MA et al. (2019) Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PlosOne. 14(5): e0216796. doi: [[10.1371/journal.pone.0216796>>https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0216796]]
82 -)))
83 -
84 -==== ====
85 -)))
QUINT_workflow_Plaques.png
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