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28	28
29	29	Use the DeepZoom app
30	30
31		-
32		-
33	33	Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
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35	35	The App will automatically generate the files for you. Monitor the progress under the "processing" tab and on the two dashboards on the left.
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40	40
41	41	Now go to the WebAlign app in order to start the registration to atlas.
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43		-[[image:Screenshot create_brain app.png]]
44	44
45	45
46		-=== Use Image service app (alt.) ===
	43	+
47	47
48		-**2b. Start the Image service UI from your webapp**
	45	+
49	49
50		-* ** Fill in the requested information:**
51		-
52		- - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
53		-
54		-E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
55		-
56		- - 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.
57		-
58		- - 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"
59		-
60		- - Or use a prefix: E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab?prefix=name_of_the_data_folder
61		-
62		- - allow the image service to access your bucket
63		-
64		-[[~[~[image:Skjermbilde 2022-02-08 103443.png~|~|height="199" width="500"~]~]>>attach:Skjermbilde 2022-02-08 103443.png]]
65		-
66		-- Store your results: Choose "create a new collab" where your ingested chunks will be stored in the bucket. This option is preferred in order not to overload the Bucket of your current  collab. Give a name to your Bucket as well as a name for the  collab (bucket slug) (see this illustration for more info)
67		-
68		-[[image:create collab.png]]
69		-
70		-- Customize your ingestion:
71		-
72		- - give a name to your ingestion in the "description of ingestion" field.
73		-
74		-* ** For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
75		-* ** Click //"preview"// in order to preview your task**
76		-* ** Click //"create task"//  to launch your ingestion**
77		-* ** Checking results in the Main UI page**
78		-
79		-Press "Task" in the higher right corner of the window.
80		-
81		-When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
82		-
83		-Otherwise, you will be redirected to the tasks list where the created task is selected.
84		-
85		-//Note! //A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"
86		-
87		-Refresh your browser in order to check the status of your task.
88		-
89		-When "successful", your chunks have been created.
90		-
91	91	== **How to use WebAlign** ==
92	92
93	93	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.