Summary

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

Details

Page properties

Content

...	...	@@ -1,31 +3,44 @@
1		-
2		-
3	3	(% class="jumbotron" %)
4	4	(((
5	5	(% class="container" %)
6	6	(((
7		-== QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images from Rodent Brain ==
	5	+== (% style="color:#16a085" %)**QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images from Rodent Brain**(%%) ==
	6	+
	7	+(% style="color:#999999" %)Neural Systems Laboratory, University of Oslo
8	8	)))
9	9	)))
10	10
11		-(% class="row" %)
	11	+==== ====
	12	+
	13	+
	14	+==== (% style="color:#c0392b" %)**Workflow Description**(%%) ====
	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:
	17	+
	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.
	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	+
	25	+==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
	26	+
	27	+* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
	28	+
12	12	(((
13		-(% class="col-xs-12 col-sm-8" %)
14		-(((
15		-(% class="wikigeneratedid" %)
16		-
	30	+As the quantifications are performed in regions defined by a reference atlas, the region definitions are standardized, allowing comparisons of data from different laboratories.
17	17
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.
20	20
21		-= What can I find here? =
	33	+==== (% style="color:#c0392b" %)**References**(%%) ====
22	22
23		-* Notice how the table of contents on the right
24		-* is automatically updated
25		-* to hold this page's headers
	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
26	26
27		-= Who has access? =
	37	+[[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/]]
28	28
29		-Describe the audience of this collab.
	39	+[[https:~~/~~/>>url:https://www.nitrc.org/projects/quicknii]][[www.nitrc.org/projects/quicknii>>url:https://www.nitrc.org/projects/quicknii]]
	40	+
	41	+[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
30	30	)))
31		-)))
	43	+
	44	+