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2	2	(((
3	3	(% class="container" %)
4	4	(((
5		-== (% style="color:#16a085" %)**QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images from Rodent Brain**(%%) ==
	5	+= My Collab's Extended Title =
6	6
7		-(% style="color:#999999" %)Neural Systems Laboratory, University of Oslo
	7	+My collab's subtitle
8	8	)))
9	9	)))
10	10
11		-==== ====
	11	+(% class="row" %)
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	13	+(% class="col-xs-12 col-sm-8" %)
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	15	+= What can I find here? =
12	12
	17	+* Notice how the table of contents on the right
	18	+* is automatically updated
	19	+* to hold this page's headers
13	13
14		-==== (% style="color:#c0392b" %)**Workflow Description**(%%) ====
	21	+= Who has access? =
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:
	23	+Describe the audience of this collab.
	24	+)))
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
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		-
24		-[[Youtube video>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
25		-
26		-==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
27		-
28		-* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
29		-
	27	+(% class="col-xs-12 col-sm-4" %)
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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.
	29	+{{box title="**Contents**"}}
	30	+{{toc/}}
	31	+{{/box}}
32	32
33		-==== (% style="color:#c0392b" %)**References**(%%) ====
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
36		-
37		-[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
38		-
39		-www.nitrc.org/projects/quicknii
40		-
41		-[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
42		-)))
43		-
44	44
	34	+)))
	35	+)))

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