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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**(%%) ==
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	7	+(% style="color:#999999" %)Neural Systems Laboratory, University of Oslo
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	11	+==== ====
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	14	+==== (% style="color:#c0392b" %)**Workflow Description**(%%) ====
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	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:
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	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.
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	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.
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	24	+[[Youtube video: https:~~/~~/www.youtube.com/watch?v=yPkAbSfla_c>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
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	26	+
	27	+==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
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	29	+* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
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	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.
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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.
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21		-= What can I find here? =
	35	+==== (% style="color:#c0392b" %)**References**(%%) ====
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	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
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27		-= Who has access? =
	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/]]
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29		-Describe the audience of this collab.
	41	+[[https:~~/~~/>>url:https://www.nitrc.org/projects/quicknii]][[www.nitrc.org/projects/quicknii>>url:https://www.nitrc.org/projects/quicknii]]
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	43	+[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
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