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1		-XWiki.sharoncy
	1	+XWiki.puchades

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4	4	(((
5	5	= QUINT demo =
6	6
7		-This collab has been set up for demo of the QUINT workflow.
	7	+This collab has been set up for demo of the online version of the QUINT workflow.
	8	+
	9	+The current integration level is basic and will improve during the remaining SGA3 period.
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15		-= What is QUINT? =
	17	+== What is QUINT? ==
16	16
17		-QUINT is a workflow for atlas-based quantification of objects such as cells in 2D histological images from mouse or rat brain.
	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]].
18	18
19		-The online version of QUINT uses several applications installed from the Collaboratory App Store. These have been pre-installed in this collab and are displayed in the panel in the top left corner.
	21	+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.
20	20
21		-1. **WebAlign: **enables registration of the image series to a reference atlas.
22		-1. **IlastikWeb:** enables extraction of objects such as cells.
23		-1. **NutilWeb: **enables quantification per atlas-region.
24		-1. **Meshview: **a 3D atlas viewer that enables visualisation of the Nutil coordinate output.
	23	+1. **[[WebAlign:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/WebAlign]] **enables registration of the 2D image series to a reference atlas.
	24	+1. [[**webilastik:**>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/webilastik]] enables extraction of objects such as cells.
	25	+1. **[[NutilWeb:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/NutilWeb]] **enables quantification of the extracted objects per atlas-region.
	26	+1. **Meshview: **enables visualisation in 3D reference space.
25	25
26		-The apps may be used separately or in sequence. The output of WebAlign and IlastikWeb are fed into NutilWeb to generate reports, images and coordinate files. The coordinates files can be viewed in Meshview.
	28	+The apps may be used separately, or in sequence for full QUINT analysis. 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.
27	27
	30	+== Demo dataset ==
28	28
29		-= How to Install Collaboratory Apps =
	32	+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.
30	30
31		-* For the purposes of this demo, the relevant apps have already been installed in the Collab.
32		-* For instructions on how to install Collaboratory Apps see...
	34	+Lillehaug, S., Syverstad, G., Nilsson, L., Bjaalie, J. G., Leergaard, T. B., & Torp, R. (2018). //Brainwide distribution and variance of amyloid-beta deposits in tg-ArcSwe mice// [Data set]. Human Brain Project Neuroinformatics Platform: https:~/~/doi.org/10.25493/G6CQ-D4D
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34		-= Who has access? =
	36	+== How to Install Collaboratory Apps ==
35	35
	38	+* For the purpose of this demo, the relevant apps have already been installed.
	39	+* Instructions for setting up the working environment, which includes installation of the Collaboratory Apps, are provided [[here>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/How%20to%20install%20Collaboratory%20Apps/]].
	40	+
	41	+== Who has access? ==
	42	+
36	36	* Collaboratory app developers
37	37	* Reviewers
38	38