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5	5	= QUINT demo =
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7		-This collab demonstrates a preliminary stage of integration of the QUINT workflow with the EBRAINS infrastructure. Following usability improvements and tighter integration of the workflow components, QUINT will be publicly released in Q3 2022.
	7	+This collab has been set up for demo of the online version of the QUINT workflow.
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	9	+The current integration level is basic and will improve during the remaining SGA3 period.
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15	15	== What is QUINT? ==
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17		-QUINT is an atlas-based workflow for quantification of cells and other features in 2-dimensional images of mouse or rat brain sections. For more information see[[ here>>https://ebrains.eu/service/quint]].
	19	+QUINT is an atlas-based workflow for quantification of cells and other features in 2-dimensional images of mouse or rat brain slices. For more information see[[ here>>https://ebrains.eu/service/quint]].
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19	19	The online version of QUINT uses several applications installed from the EBRAINS Collaboratory App Store. These have been pre-installed in this collab and are displayed in the navigation panel (on the left-hand side in desktop browsers). Instructions for using the apps are also provided.
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24	24	1. **[[NutilWeb:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/NutilWeb]] **enables quantification of the extracted objects per atlas-region.
25	25	1. [[**Meshview: **>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/Meshview]]enables visualisation in 3D reference space.
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27		-The apps may be used separately, or in sequence for full QUINT analysis. File transfer between the apps is done through the Bucket.
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29		-As the first step, the images to be analysed are uploaded to the Bucket. The Image Service is used to convert them to formats that are compatible with WebAlign and webilastik. The result of WebAlign and Webilastik are fed into NutilWeb, which generates reports, plots, overlay images and coordinate files that can be downloaded from the Collab Bucket. The coordinates files may be viewed in Meshview.
	30	+The apps may be used separately, or in sequence for full QUINT analysis.
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	32	+The Image Service is used to convert the images to formats that are compatible with WebAlign and webilastik. The output of WebAlign and Webilastik are fed into NutilWeb, which generates reports, plots, overlay images and coordinate files that can be downloaded from the Collab Bucket. The coordinates files may be viewed in Meshview. File transfer between the apps is done through the Bucket.
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31	31	== Demo dataset ==
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33	33	A demo dataset for use with the apps is provided in the Bucket. The demo material originates from histological section images from the transgenic Arctic / Swedish mouse model of Alzheimer's disease.