Wiki source code of QUINT demo

Version 16.1 by sharoncy on 2021/12/08 11:19
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sharoncy 5.1 5 = QUINT demo =
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sharoncy 11.1 7 This collab has been set up for demo of the QUINT workflow.
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sharoncy 14.1 15 = What is QUINT? =
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sharoncy 10.1 18 QUINT is a workflow for atlas-based quantification of objects such as cells in 2D histological images from mouse or rat brain.
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sharoncy 10.1 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.
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sharoncy 10.1 22 1. **WebAlign: **enables registration of the image series to a reference atlas.
23 1. **IlastikWeb:** enables extraction of objects such as cells.
24 1. **NutilWeb: **enables quantification per atlas-region.
25 1. **Meshview: **a 3D atlas viewer that enables visualisation of the Nutil coordinate output.
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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.
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sharoncy 13.1 30 = How to Install Collaboratory Apps =
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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...
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sharoncy 1.1 35 = Who has access? =
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sharoncy 7.1 37 * Collaboratory app developers
38 * Reviewers
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46 {{box title="**Contents**"}}
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