Last modified by puchades on 2022/11/02 10:16
From version 63.1
edited by puchades
on 2021/10/18 09:38
Change comment: There is no comment for this version
To version 8.1
edited by sharoncy
on 2020/03/09 13:53
Change comment: There is no comment for this version

Summary

Details

Page properties
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.puchades
1 +XWiki.sharoncy
Content
... ... @@ -1,69 +1,31 @@
1 -(% class="box infomessage" %)
2 -(((
3 -Online documentation: - [[https:~~/~~/quicknii.readthedocs.io/en/latest/index.html>>https://quicknii.readthedocs.io/en/latest/index.html]] [[-https:~~/~~/visualign.readthedocs.io/en/latest/index.html#>>https://visualign.readthedocs.io/en/latest/index.html#]][[ -https:~~/~~/nutil.readthedocs.io/en/latest/index.html>>https://nutil.readthedocs.io/en/latest/index.html]]
4 -)))
1 +
5 5  
6 -Please, address your questions about our tools and workflows to [[https:~~/~~/ebrains.eu/support/>>https://ebrains.eu/support/]].
7 -
8 -[[image:User_support_Ebrains.png]]
9 -
10 -
11 -[[image:QUINT_workflow_Plaques.png||style="float:left"]]
12 -
13 -== (% style="color:#c0392b" %)**Description**(%%) ==
14 -
15 -**The QUINT workflow enables an atlas-based analysis of extracted features from histological image sections from the rodent brain by using 3D reference atlases. **
16 -
17 -**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.**
18 -
19 -The workflow is built on the following open-access software.
20 -
21 -* [[(% 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.
22 -* [[(% 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.
23 -* //[[(% 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.
24 -* (% 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//.
25 -
26 -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.
27 -
28 -[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
29 -
30 -
31 -
32 -
33 -
34 -
35 -
36 -
37 -
38 -
39 -
40 -
41 -
42 -
43 -
44 -QUINT workflow video
45 -
46 -== (% style="color:#c0392b" %)**Workflow highlights**(%%) ==
47 -
48 -(% class="box successmessage" %)
3 +(% class="jumbotron" %)
49 49  (((
50 -The semi-automated QUINT workflow uses open-access software that can be operated without any scripting knowledge.
5 +(% class="container" %)
6 +(((
7 +== QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images from Rodent Brain ==
51 51  )))
9 +)))
52 52  
11 +(% class="row" %)
53 53  (((
54 -(% class="box successmessage" %)
13 +(% class="col-xs-12 col-sm-8" %)
55 55  (((
56 -Because the quantifications are performed in regions defined by a reference atlas, the region definitions are standardised, allowing comparisons of data from different laboratories.
57 -)))
15 +(% class="wikigeneratedid" %)
16 +
58 58  
59 -==== (% style="color:#c0392b" %)**References**(%%) ====
18 +(% class="wikigeneratedid" id="H" %)
19 +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. The first – ilastik - allows the extraction of labelled features such as cells by segmentation. The second – QuickNII - generates atlas maps customised to match the proportions and cutting plane of the brain sections. The third – Nutil – enables quantification and spatial analysis of features by drawing on the output of ilastik and QuickNII. 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.
60 60  
61 -* 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]]
62 -* 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]]
63 -* 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]]
64 -* (((
65 -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]]
66 -)))
21 += What can I find here? =
67 67  
68 -==== ====
23 +* Notice how the table of contents on the right
24 +* is automatically updated
25 +* to hold this page's headers
26 +
27 += Who has access? =
28 +
29 +Describe the audience of this collab.
69 69  )))
31 +)))
QUINT_workflow_Plaques.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.puchades
Size
... ... @@ -1,1 +1,0 @@
1 -213.7 KB
Content
QUINT_workflow_pic.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.puchades
Size
... ... @@ -1,1 +1,0 @@
1 -252.6 KB
Content
Youtube_QUINT.PNG
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.puchades
Size
... ... @@ -1,1 +1,0 @@
1 -1.1 MB
Content
Collaboratory.Apps.Collab.Code.CollabClass[0]
Public
... ... @@ -1,1 +1,1 @@
1 -Yes
1 +No
XWiki.XWikiRights[7]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Levels
... ... @@ -1,1 +1,0 @@
1 -view
Users
... ... @@ -1,1 +1,0 @@
1 -XWiki.XWikiGuest
XWiki.XWikiRights[8]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Groups
... ... @@ -1,1 +1,0 @@
1 -XWiki.XWikiAllGroup
Levels
... ... @@ -1,1 +1,0 @@
1 -view