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4	4	(((
5	5	= QUINT demo =
6	6
7		-This collab has been set up for demo of the online version of the QUINT workflow.
	7	+This collab has been set up for demo of the QUINT workflow.
8	8	)))
9	9	)))
10	10
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15	15	= What is QUINT? =
16	16
17	17
18		-QUINT is a workflow for atlas-based quantification of objects such as cells in 2D histological images from mouse or rat brain. For more information see the EBRAINS [[QUINT service>>https://ebrains.eu/service/quint]] page.
	18	+QUINT is a workflow for atlas-based quantification of objects such as cells in 2D histological images from mouse or rat brain.
19	19
20		-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 panel in the top left corner. Instructions for using the apps are also provided.
	20	+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	21
22		-1. **[[WebAlign:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/WebAlign]] **enables registration of the 2D image series to a reference atlas.
	22	+1. **WebAlign: **enables registration of the image series to a reference atlas.
23	23	1. **IlastikWeb:** enables extraction of objects such as cells.
24		-1. **[[NutilWeb:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/NutilWeb]] **enables quantification per atlas-region.
25		-1. **Meshview: **enables visualisation of the Nutil coordinate output.
	24	+1. **NutilWeb: **enables quantification per atlas-region.
	25	+1. **Meshview: **a 3D atlas viewer that enables visualisation of the Nutil coordinate output.
26	26
27		-The apps may be used separately, or in sequence for full QUINT analysis. The output of WebAlign and IlastikWeb are fed into NutilWeb, which generates reports, images and coordinate files. The coordinates files can be viewed in Meshview. File transfer between the apps is done through the Collab Bucket.
	27	+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	28
29	29
30	30	= How to Install Collaboratory Apps =
31	31
32		-* For the purpose of this demo, the relevant apps have already been installed.
33		-* 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/]].
	32	+* For the purposes of this demo, the relevant apps have already been installed in the Collab.
	33	+* For instructions on how to install Collaboratory Apps see...
34	34
35	35	= Who has access? =
36	36