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  • create series webAlign.png

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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	+=== Opening a private dataset ===
	224	+
	225	+1. Navigate to the WebWarp app in the left-hand panel: all the .waln files located in the Bucket are displayed on the WebWarp main page.
	226	+1. Select the waln file corresponding to your result from the WebAlign image registration.
	227	+1. Wait for the images to load: this may take some time.
	228	+
	229	+=== Opening an EBRAINS dataset ===
	230	+
	231	+If you would like to work with an EBRAINS dataset, open the LocaliZoom link from the KG dataset card ( [[https:~~/~~/search.kg.ebrains.eu>>url:https://search.kg.ebrains.eu]]) and paste it in the "Import LocaliZoom link" tab in WebAlign. Save this series as a .waln file you then can open in WebWarp.

create series webAlign.png

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