Last modified by puchades on 2022/11/02 10:16
From version 27.1
edited by sharoncy
on 2020/03/09 14:37
Change comment: There is no comment for this version
To version 67.1
edited by sharoncy
on 2021/10/18 09:45
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -1,44 +1,85 @@
1 -(% class="jumbotron" %)
1 +(% class="box infomessage" %)
2 2  (((
3 -(% class="container" %)
4 -(((
5 -== (% style="color:#16a085" %)**QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images from Rodent Brain**(%%) ==
3 +==== Online documentation ====
6 6  
7 -(% style="color:#999999" %)Neural Systems Laboratory, University of Oslo
5 +[[QuickNII user documentation>>https://quicknii.readthedocs.io/en/latest/index.html]]
6 +
7 +[[VisuAlign user documentation>>https://visualign.readthedocs.io/en/latest/index.html]]
8 +
9 +[[Ilastik user documentation>>https://nutil.readthedocs.io/en/latest/Ilastik.html]]
10 +
11 +[[Nutil user documentation>>https://nutil.readthedocs.io/en/latest/index.html]]                                                                   
8 8  )))
9 -)))
10 10  
11 -==== ====
12 12  
15 +[[image:QUINT_workflow_Plaques.png||height="470" style="float:left" width="1277"]]
13 13  
14 -==== (% style="color:#c0392b" %)**Workflow Description**(%%) ====
17 +== ==
15 15  
16 -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:
19 +== ==
17 17  
18 -1. [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells by segmentation.
19 -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.
20 -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.
21 +== ==
21 21  
22 -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.
23 +== ==
23 23  
24 -[[Youtube video>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
25 +== ==
25 25  
26 -==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
27 +== ==
27 27  
28 -* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
29 +== (% style="color:#c0392b" %)**Description**(%%) ==
29 29  
30 -(((
31 -* As the quantifications are performed in regions defined by a reference atlas, the region definitions are standardized, allowing comparisons of data from different laboratories.
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 -==== (% style="color:#c0392b" %)**References**(%%) ====
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.**
34 34  
35 -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
35 +The workflow is built on the following open-access software.
36 36  
37 -[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
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//.
38 38  
39 -[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
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.
40 40  
41 -[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
44 +[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
45 +
46 +
47 +
48 +
49 +
50 +
51 +
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.
42 42  )))
43 43  
44 -
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
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.puchades
Size
... ... @@ -1,0 +1,1 @@
1 +213.7 KB
Content
QUINT_workflow_pic.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.puchades
Size
... ... @@ -1,0 +1,1 @@
1 +252.6 KB
Content
Youtube_QUINT.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.puchades
Size
... ... @@ -1,0 +1,1 @@
1 +1.1 MB
Content
Collaboratory.Apps.Collab.Code.CollabClass[0]
Public
... ... @@ -1,1 +1,1 @@
1 -No
1 +Yes
XWiki.XWikiRights[7]
Allow/Deny
... ... @@ -1,0 +1,1 @@
1 +Allow
Levels
... ... @@ -1,0 +1,1 @@
1 +view
Users
... ... @@ -1,0 +1,1 @@
1 +XWiki.XWikiGuest
XWiki.XWikiRights[8]
Allow/Deny
... ... @@ -1,0 +1,1 @@
1 +Allow
Groups
... ... @@ -1,0 +1,1 @@
1 +XWiki.XWikiAllGroup
Levels
... ... @@ -1,0 +1,1 @@
1 +view