Last modified by puchades on 2025/02/13 10:43
From version 4.1
edited by puchades
on 2023/04/12 11:40
Change comment: There is no comment for this version
To version 7.1
edited by puchades
on 2023/04/21 13:41
Change comment: There is no comment for this version

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1 -== To set up the working environment: ==
1 +== To set up your working environment: ==
2 2  
3 3  1. [[Register>>url:https://ebrains.eu/register/]] for an EBRAINS account, login, and set up a [[private collab>>url:https://wiki.ebrains.eu/bin/view/Collabs/]].
4 4  1. Initialise the Bucket by clicking on Bucket in the navigation panel -> Create Bucket.
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29 29  
30 30   - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
31 31  
32 -E.g. https:~/~/data-proxy.ebrains.eu/api/buckets/name-of-my-collab
32 +E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
33 33  
34 - - you can filter the data using RegEx expressions. E.g. name_of_the_data_folder\/.*\.jpg$ (for filtering jpeg files only).
34 + - you can filter the data using RegEx expressions. E.g. name_of_the_data_file.*\.jpg$ (for filtering jpeg files only). Or e.g hbp-00173_262_1366_1827.*\.tif$ for tiff files.
35 35  
36 36   - If your URL is valid, you will see the list of files by pressing "yes". Paste the name of the file you want to select. You can go back to the previous step  by pressing "back"
37 37  
38 - - Or use a prefix: E.g. https:~/~/data-proxy.ebrains.eu/api/buckets/name-of-my-collab?prefix=name_of_the_data_folder
38 + - Or use a prefix: E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab?prefix=name_of_the_data_folder
39 39  
40 40   - allow the image service to access your bucket
41 41  
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71 71  
72 72  == **How to use WebAlign** ==
73 73  
74 +WebAlign is an online tool for spatial registration of histological section images from rodent brains to reference 3D atlases.  Different experimental datasets registered to the same reference atlas allows you to spatially integrate, analyse and navigate these datasets within a standardised coordinate system. The output of WebAlign can be used for analysis in the online QUINT workflow.
75 +
74 74  The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
75 75  
76 76  === Opening a sample dataset ===
77 77  
78 -Demo dataset is loaded using the file:**demo_mouse_data_start**
80 +Demo dataset is loaded using the file: **demo_mouse_data_start**
79 79  
80 80  You can see the result of a finished anchoring by choosing the file: **demo_mouse_data**
81 81