Last modified by puchades on 2025/02/13 10:43
From version 24.1
edited by puchades
on 2023/06/21 10:58
Change comment: There is no comment for this version
To version 33.2
edited by puchades
on 2023/06/21 15:46
Change comment: There is no comment for this version

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99 99  
100 100  === Opening a sample dataset ===
101 101  
102 -Demo dataset is loaded using the file: **demo_mouse_data_start**
102 +Demo dataset is loaded using the file: **demo_mouse_data_start.waln**
103 103  
104 -You can see the result of a finished anchoring by choosing the file: **demo_mouse_data**
104 +You can see the result of a finished anchoring by choosing the file: **demo_mouse_data.waln**
105 105  
106 106  === Opening a private dataset ===
107 107  
108 -After you have uploaded your images to the bucket and ingested your images with the Image service, this has generated DZI chunks. These DZI files are used by WebAlign.
108 +After you have uploaded your images to the bucket and ingested your images with the QUINT Image creator app, this has generated DZIP chunks. These DZIP files are used by WebAlign.
109 109  
110 110  ~1. Start a new registration by pressing "create new series", the UI will ask you for the name of the collab where DZI chunks are stored. E.g. my-collab-name
111 111  
112 -2. WebAlign will search for DZI files and list those found.
112 +2. WebAlign will search for DZIP files and list those found.
113 113  
114 114  3. Enter a name for the descriptor json file which will be created and will contain your anchoring information.
115 115  
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117 117  
118 118  5. Press //"create"//. The main window will now display WebAlign. This step can take some time.
119 119  
120 +[[image:create series webAlign.png]]
121 +
122 +=== Opening an EBRAINS dataset ===
123 +
124 +(% class="wikigeneratedid" %)
125 +If you would like to work with an EBRAINS dataset, fetch the LocaliZoom link from the KG dataset card ( [[https:~~/~~/search.kg.ebrains.eu>>https://search.kg.ebrains.eu]] )and paste it in the "Import LocaliZoom link" tab.
126 +
127 +(% class="wikigeneratedid" %)
128 +These series already have been registered to a reference atlas, so this gives you a starting point. The linear registrations obtained with WebAlign can be refined using WebWarp.
129 +
120 120  === Registration instructions ===
121 121  
122 122  **Short keys**
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194 194  
195 195  Drag the midpoint around to move the cut.
196 196  
197 -Drag anywhere else to rotate the cut (inside the given standard plane, around the midpoint)
207 +Drag anywhere else to rotate the cut (inside the given standard plane, around the midpoint).
208 +
209 +== **How to use WebWarp** ==
210 +
211 +WebWarp is an online tool for nonlinear refinement of spatial registration of histological section images from rodent brains to reference 3D atlases. Webwarp is compatible with registration performed with the WebAlign tool. Different experimental datasets registered to the same reference atlas allows you to spatially integrate, analyse and navigate these datasets within a standardised coordinate system.
212 +
213 +Online user manual: [[https:~~/~~/webwarp.readthedocs.io/en/latest/>>https://webwarp.readthedocs.io/en/latest/]]
214 +
215 +The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
216 +
217 +=== Opening a sample dataset ===
218 +
219 +Demo dataset is loaded using the file: **demo_mouse_data.waln**
220 +
221 +You can see the result of a finished anchoring by choosing the file: **demo_mouse_data.wwrp**
222 +
223 +
create series webAlign.png
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1 +XWiki.puchades
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