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5	5	= QUINT demo =
6	6
7	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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17		-== What is QUINT? ==
	15	+= What is QUINT? =
18	18
19		-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]].
20	20
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.
	18	+QUINT is a workflow for atlas-based quantification of objects such as cells in 2D histological images from mouse or rat brain.
22	22
23		-1. **[[Image Service:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/Image%20Service]]** convert your image series to formats compatible with QUINT.
24		-1. **[[WebAlign:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/WebAlign]] **enables registration of the 2D image series to a 3D reference atlas.
25		-1. [[**webilastik:**>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/webilastik]] enables extraction of objects such as cells from the image series.
26		-1. **[[NutilWeb:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/NutilWeb]] **enables quantification of the extracted objects per atlas-region.
27		-1. [[**Meshview: **>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/Meshview]]enables visualisation in 3D reference space.
	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.
28	28
29		-The apps may be used separately, or in sequence for full QUINT analysis. File transfer between the apps is done through the Bucket.
	22	+1. **[[WebAlign:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/WebAlign]] **enables registration of the 2D image series to a reference atlas.
	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.
30	30
31		-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.
	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>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/Bucket]].
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33		-== Demo dataset ==
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35		-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	+= How to Install Collaboratory Apps =
36	36
37		-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
	32	+* For the purposes of this demo, the relevant apps have already been installed in the Collab.
	33	+* Instructions for setting up the working environment, whicn includes installing the collaboratory apps, are provided [[here>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/How%20to%20install%20Collaboratory%20Apps/]].
38	38
39		-== How to Install Collaboratory Apps ==
	35	+= Who has access? =
40	40
41		-* For the purpose of this demo, the relevant apps have already been installed.
42		-* 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/]].
43		-
44		-== Who has access? ==
45		-
46	46	* Collaboratory app developers
47	47	* Reviewers
48	48