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13	13	==== ====
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16		-==== (% style="color:#c0392b" %)Workflow Description(%%) ====
	14	+==== (% style="color:#c0392b" %)**Workflow Description**(%%) ====
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18	18	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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20		-1. ilastik allows the extraction of labelled features such as cells by segmentation.
21		-1. QuickNII generates atlas maps customised to match the proportions and cutting plane of the brain sections.
22		-1. Nutil enables quantification and spatial analysis of features by drawing on the output of ilastik and QuickNII.
	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.
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24	24	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]]
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	26	+==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
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	28	+* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
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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.
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	33	+==== (% style="color:#c0392b" %)**References**(%%) ====
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	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
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	37	+[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
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	39	+[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
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	41	+[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
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