Last modified by puchades on 2025/02/13 10:43
From version 9.1
edited by puchades
on 2023/06/21 10:19
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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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10 10  1. To install Collaboratory Apps, click on the + Create button (top right corner).
11 11  1. Give the page a Title (for example, WebAlign), select the Community App option, and click Create.
12 12  1. Select the App to install (for example, WebAlign), and click Save and View.
13 -1. Repeat this for all the relevant Community Apps.
13 +1. Repeat this for all the relevant Community Apps. You will need, "QUINT Image creator app"; "WebAlign"; "WebWarp"; "LocaliZoom" and "MeshView".
14 14  1. Navigate between the Apps in the navigation panel. File transfer between the Apps is through the Bucket.
15 15  
16 16  == How to prepare your images? ==
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27 27  
28 28  Two alternatives are available, the QUINT image creator app, which is automatically creating the necessary files for downstream analyses in your collab. Or, you can use the image service app which is able to create image tiles in different formats. The steps for preparing your files are described bellow:
29 29  
30 -(% class="wikigeneratedid" %)
31 -=== ===
32 -
33 33  === Use the "QUINT image creator" app ===
34 34  
35 -**~1. Select images to ingest**
32 +**2a. Select images to ingest**
36 36  
37 -Shift-Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
34 +Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
38 38  
39 39  The App will automatically generate the files for you. Monitor the progress under the "processing" tab and on the two dashboards on the left.
40 40  
... ... @@ -42,17 +42,17 @@
42 42  
43 43  Click on the "View Brain" button in order to preview your images.
44 44  
42 +Now go to the WebAlign app in order to start the registration to atlas.
45 45  
44 +[[image:Screenshot create_brain app.png]]
46 46  
47 47  
48 -== ==
47 +=== Use Image service app (alt.) ===
49 49  
50 -=== Use Image service app ===
49 +**2b. Start the Image service UI from your webapp**
51 51  
52 -**~1. Start the Image service UI from your webapp**
51 +* ** Fill in the requested information:**
53 53  
54 -**2. Fill in the requested information:**
55 -
56 56   - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
57 57  
58 58  E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
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65 65  
66 66   - allow the image service to access your bucket
67 67  
68 -[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]
65 +[[[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]>>attach:Skjermbilde 2022-02-08 103443.png]]
69 69  
70 70  - 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)
71 71  
72 -[[image:create collab.png||height="427" width="900"]]
69 +[[image:create collab.png]]
73 73  
74 74  - Customize your ingestion:
75 75  
76 76   - give a name to your ingestion in the "description of ingestion" field.
77 77  
78 -**3. For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
75 +* ** For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
76 +* ** Click //"preview"// in order to preview your task**
77 +* ** Click //"create task"//  to launch your ingestion**
78 +* ** Checking results in the Main UI page**
79 79  
80 -**4. Click //"preview"// in order to preview your task**
81 -
82 -**5. Click //"create task"//  to launch your ingestion**
83 -
84 -**6. Checking results in the Main UI page**
85 -
86 86  Press "Task" in the higher right corner of the window.
87 87  
88 88  When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
... ... @@ -95,114 +95,6 @@
95 95  
96 96  When "successful", your chunks have been created.
97 97  
98 -== ==
99 -
100 -=== Use Image service app ===
101 -
102 -**~1. Start the Image service UI from your webapp**
103 -
104 -**2. Fill in the requested information:**
105 -
106 - - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
107 -
108 -E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
109 -
110 - - 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.
111 -
112 - - 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"
113 -
114 - - Or use a prefix: E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab?prefix=name_of_the_data_folder
115 -
116 - - allow the image service to access your bucket
117 -
118 -[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]
119 -
120 -- 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)
121 -
122 -[[image:create collab.png||height="427" width="900"]]
123 -
124 -- Customize your ingestion:
125 -
126 - - give a name to your ingestion in the "description of ingestion" field.
127 -
128 -**3. For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
129 -
130 -**4. Click //"preview"// in order to preview your task**
131 -
132 -**5. Click //"create task"//  to launch your ingestion**
133 -
134 -**6. Checking results in the Main UI page**
135 -
136 -Press "Task" in the higher right corner of the window.
137 -
138 -When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
139 -
140 -Otherwise, you will be redirected to the tasks list where the created task is selected.
141 -
142 -//Note! //A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"
143 -
144 -Refresh your browser in order to check the status of your task.
145 -
146 -When "successful", your chunks have been created.
147 -
148 -== ==
149 -
150 -=== Use Image service app ===
151 -
152 -**~1. Prepare your images before upload by naming them according this naming convention:**
153 -
154 -The ID should be unique to the particular brain section and in the format sXXX, with XXX representing the section number. The section number should reflect the serial order and spacing of the sections (e.g., s002, s006, s010 for every 4^^th^^ section starting with section 2).
155 -
156 -Example: tg2345_MMSH_s001_segmentation.png
157 -
158 -- Upload the images you want to work with into the bucket of your collab using the Data proxy (press on //"Bucket"//)
159 -
160 -**2. Start the Image service UI from your webapp**
161 -
162 -**3. Fill in the requested information:**
163 -
164 - - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
165 -
166 -E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
167 -
168 - - 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.
169 -
170 - - 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"
171 -
172 - - Or use a prefix: E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab?prefix=name_of_the_data_folder
173 -
174 - - allow the image service to access your bucket
175 -
176 -[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]
177 -
178 -- 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)
179 -
180 -[[image:create collab.png||height="427" width="900"]]
181 -
182 -- Customize your ingestion:
183 -
184 - - give a name to your ingestion in the "description of ingestion" field.
185 -
186 -**3. For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
187 -
188 -**4. Click //"preview"// in order to preview your task**
189 -
190 -**5. Click //"create task"//  to launch your ingestion**
191 -
192 -**6. Checking results in the Main UI page**
193 -
194 -Press "Task" in the higher right corner of the window.
195 -
196 -When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
197 -
198 -Otherwise, you will be redirected to the tasks list where the created task is selected.
199 -
200 -//Note! //A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"
201 -
202 -Refresh your browser in order to check the status of your task.
203 -
204 -When "successful", your chunks have been created.
205 -
206 206  == **How to use WebAlign** ==
207 207  
208 208  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.
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213 213  
214 214  === Opening a sample dataset ===
215 215  
216 -Demo dataset is loaded using the file: **demo_mouse_data_start**
102 +Demo dataset is loaded using the file: **demo_mouse_data_start.waln**
217 217  
218 -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**
219 219  
220 220  === Opening a private dataset ===
221 221  
222 -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.
223 223  
224 224  ~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
225 225  
226 -2. WebAlign will search for DZI files and list those found.
112 +2. WebAlign will search for DZIP files and list those found.
227 227  
228 228  3. Enter a name for the descriptor json file which will be created and will contain your anchoring information.
229 229  
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231 231  
232 232  5. Press //"create"//. The main window will now display WebAlign. This step can take some time.
233 233  
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 +
234 234  === Registration instructions ===
235 235  
236 236  **Short keys**
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308 308  
309 309  Drag the midpoint around to move the cut.
310 310  
311 -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 +
Screenshot create_brain app.png
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