Wiki source code of QUINT demo collab
Hide last authors
| author | version | line-number | content |
|---|---|---|---|
 |
1.1 | 1 | (% class="jumbotron" %) |
| 2 | ((( | ||
| 3 | (% class="container" %) | ||
| 4 | ((( | ||
| |
5.1 | 5 | = QUINT demo = |
| |
1.1 | 6 | |
| |
52.1 | 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. |
| |
1.1 | 8 | ))) |
| 9 | ))) | ||
| 10 | |||
| 11 | (% class="row" %) | ||
| 12 | ((( | ||
| 13 | (% class="col-xs-12 col-sm-8" %) | ||
| 14 | ((( | ||
| |
56.1 | 15 | (% class="box warningmessage" %) |
| 16 | ((( | ||
| 17 | We have identified a bug when using the Safari web browser. Please use another one. | ||
| 18 | ))) | ||
| 19 | |||
| |
57.1 | 20 | (% class="box warningmessage" id="H" %) |
| 21 | ((( | ||
| 22 | Users of other browsers may also encounter a warning message meant for Safari users. Should it happen, please empty the browser cache. | ||
| 23 | ))) | ||
| |
56.1 | 24 | |
| 25 | {{box title="**Contents**"}} | ||
| 26 | {{toc/}} | ||
| 27 | {{/box}} | ||
| 28 | |||
| |
39.1 | 29 | == What is QUINT? == |
| |
1.1 | 30 | |
| |
50.1 | 31 | 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]]. |
| |
1.1 | 32 | |
| |
53.1 | 33 | The web 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. |
| |
7.1 | 34 | |
| |
47.1 | 35 | 1. **[[Image Service:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/Image%20Service]]** convert your image series to formats compatible with QUINT. |
| |
46.1 | 36 | 1. **[[WebAlign:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/WebAlign]] **enables registration of the 2D image series to a 3D reference atlas. |
| 37 | 1. [[**webilastik:**>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/webilastik]] enables extraction of objects such as cells from the image series. | ||
| |
35.1 | 38 | 1. **[[NutilWeb:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/NutilWeb]] **enables quantification of the extracted objects per atlas-region. |
| |
43.1 | 39 | 1. [[**Meshview: **>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/Meshview]]enables visualisation in 3D reference space. |
| |
10.1 | 40 | |
| |
50.1 | 41 | The apps may be used separately, or in sequence for full QUINT analysis. File transfer between the apps is done through the Bucket. |
| |
49.1 | 42 | |
| |
50.1 | 43 | 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. |
| |
10.1 | 44 | |
| |
40.1 | 45 | == Demo dataset == |
| |
36.1 | 46 | |
| |
40.1 | 47 | 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. |
| |
36.1 | 48 | |
| |
37.1 | 49 | 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 |
| 50 | |||
| |
39.1 | 51 | == How to Install Collaboratory Apps == |
| |
10.1 | 52 | |
| |
24.1 | 53 | * For the purpose of this demo, the relevant apps have already been installed. |
| 54 | * 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/]]. | ||
| |
10.1 | 55 | |
| |
39.1 | 56 | == Who has access? == |
| |
1.1 | 57 | |
| |
7.1 | 58 | * Collaboratory app developers |
| 59 | * Reviewers | ||
| 60 | |||
| 61 | |||
| |
1.1 | 62 | ))) |
| 63 | |||
| 64 | (% class="col-xs-12 col-sm-4" %) | ||
| 65 | ((( | ||
| 66 | |||
| 67 | ))) | ||
| 68 | ))) |