Summary

• Page properties (1 modified, 0 added, 0 removed)

Details

Page properties

Content

...	...	@@ -2,34 +2,45 @@
2	2	(((
3	3	(% class="container" %)
4	4	(((
5		-= My Collab's Extended Title =
	5	+== (% style="color:#16a085" %)**QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images from Rodent Brain**(%%) ==
6	6
7		-My collab's subtitle
	7	+(% style="color:#999999" %)Neural Systems Laboratory, University of Oslo
8	8	)))
9	9	)))
10	10
11		-(% class="row" %)
12		-(((
13		-(% class="col-xs-12 col-sm-8" %)
14		-(((
15		-= What can I find here? =
	11	+==== ====
16	16
17		-* Notice how the table of contents on the right
18		-* is automatically updated
19		-* to hold this page's headers
20	20
21		-= Who has access? =
	14	+==== (% style="color:#c0392b" %)**Workflow Description**(%%) ====
22	22
23		-Describe the audience of this collab.
24		-)))
	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:
25	25
	18	+1. (% style="color:#2980b9" %)//ilastik//(%%) allows the extraction of labelled features such as cells by segmentation.
	19	+1. (% style="color:#2980b9" %)//QuickNII//(%%) generates atlas maps customised to match the proportions and cutting plane of the brain sections.
	20	+1. (% style="color:#2980b9" %)//Nutil//(%%) enables image transformations, in addition to quantification and spatial analysis of features by drawing on the output of ilastik and QuickNII.
26	26
27		-(% class="col-xs-12 col-sm-4" %)
	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>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
	25	+
	26	+
	27	+==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
	28	+
	29	+* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
	30	+
28	28	(((
29		-{{box title="**Contents**"}}
30		-{{toc/}}
31		-{{/box}}
	32	+As the quantifications are performed in regions defined by a reference atlas, the region definitions are standardized, allowing comparisons of data from different laboratories.
32	32
33		-
	34	+
	35	+==== (% style="color:#c0392b" %)**References**(%%) ====
	36	+
	37	+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
	38	+
	39	+[[https>>url:https://www.nitrc.org/projects/nutil/]][[:~~/~~/www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/nutil/]]
	40	+
	41	+[[https:~~/~~/>>url:https://www.nitrc.org/projects/quicknii]][[www.nitrc.org/projects/quicknii>>url:https://www.nitrc.org/projects/quicknii]]
	42	+
	43	+[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
34	34	)))
35		-)))
	45	+
	46	+