Version 54.1 by puchades on 2025/02/13 10:00
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1 == To set up your working environment: ==
2
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 1. Initialise the Bucket by clicking on Bucket in the navigation panel -> Create Bucket.
5 1. Remember to set your data proxy bucket to "public". Your collab can still be private.
6 1. Give users Admin, Editor or Viewer rights by clicking** Team** in the navigation panel.
7 1. Install WebAlign, WebWarp, LocaliZoom, and Meshview from the EBRAINS Collaboratory App Store (see instructions below)[[image:public_data_proxy_bucket.png]]
8
9 == How to install Collaboratory Apps ==
10
11 1. To install Collaboratory Apps, click on the + Create button (top right corner).
12 1. Give the page a Title (for example, WebAlign), select the Community App option, and click Create.
13 1. Select the App to install (for example, WebAlign), and click Save and View.
14 1. Repeat this for all the relevant Community Apps. You will need, "QUINT Image creator app"; "WebAlign"; "WebWarp"; "LocaliZoom" and "MeshView".
15 1. Navigate between the Apps in the navigation panel. File transfer between the Apps is through the Bucket.
16
17 == How to prepare your images? ==
18
19 **~1. Prepare your images before upload by naming them according this naming convention:**
20
21 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).
22
23 Example: tg2345_MMSH_s001.tif
24
25 - Upload the images you want to work with into the bucket of your collab using the Data proxy (press on //"Bucket"//)
26
27 **2. Image ingestion**
28
29 Use the DeepZoom app
30
31
32
33 Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
34
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.
36
37 When the ingestion is finished, your serie will appear under the "Prepared Brains" tab.
38
39 Click on the "View Brain" button in order to preview your images.
40
41 Now go to the WebAlign app in order to start the registration to atlas.
42
43 [[image:Screenshot create_brain app.png]]
44
45
46 === Use Image service app (alt.) ===
47
48 **2b. Start the Image service UI from your webapp**
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 == **How to use WebAlign** ==
92
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.
94
95 Online user manual: [[https:~~/~~/webalign.readthedocs.io/en/latest/>>https://webalign.readthedocs.io/en/latest/]]
96
97 The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
98
99 === Opening a sample dataset ===
100
101 Demo dataset is loaded using the file: **demo_mouse_data_start.waln**
102
103 You can see the result of a finished anchoring by choosing the file: **demo_mouse_data.waln**
104
105 === Opening a private dataset ===
106
107 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.
108
109 ~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
110
111 2. WebAlign will search for DZIP files and list those found.
112
113 3. Enter a name for the descriptor json file which will be created and will contain your anchoring information.
114
115 4. Choose the target 3D reference atlas (WHSv3 for Rat and CCFv3_2017 for Mouse).
116
117 5. Press //"create"//. The main window will now display WebAlign. This step can take some time.
118
119 [[image:create series webAlign.png]]
120
121 === Opening an EBRAINS dataset ===
122
123 (% class="wikigeneratedid" %)
124 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.
125
126 (% class="wikigeneratedid" %)
127 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.
128
129 === Registration instructions ===
130
131 **Short keys**
132
133 |=To do this|=Press|=Description
134 |Place marker|Space bar|Markers are the anchor points of most transformations (stretch and rotate).
135 |Remove marker|Esc|Removes a previously placed marker.
136 |Horizontal stretch from marker |Left/Right arrow keys|Marker becomes a vertical line, and mouse drag horizontally resizes the cut.
137 |Vertical stretch from marker |Up/Down arrow keys|Marker becomes a horizontal line, and mouse drag vertically resizes the cut
138 |Rotate around marker|PgUp/PgDown|Marker becomes a cross with a surrounding arc, and mouse drag rotates the cut.
139 |In plane adjust |Click + drag|If there is no marker, or the marker is a cross, mouse drag slides the cut in its plane (translation).
140
141 **Start the registration**
142
143 The main window shows the selected image with the atlas overlay.
144
145 -If necessary, change the atlas from coronal view to sagittal or horizontal view (see Navigation panel below)
146
147 ~1. Move the atlas to the approximate position of your section using the yellow dots in the three small windows from the navigation panel.
148
149 2. Start anchoring by placing a marker with the //"Space bar//" , it is initially a cross, and it is the fix point of (most) transformations. The "//Escape key//" can be used to remove the marker.
150
151 3. The main window supports mouse drag in multiple modes in order to stretch the atlas and find the correct position.
152
153 -If there is no marker, or the marker is a cross, mouse drag slides the cut in its plane (translation).
154
155 -Keyboard controls to modify mouse drag (they also place the marker if it's not placed already):
156
157 -Left/Right arrow keys: marker becomes a vertical line, and mouse drag horizontally resizes the cut
158
159 -Up/Down arrow keys: marker becomes a horizontal line, and mouse drag vertically resizes the cut
160
161 -PgUp/PgDown keys: marker becomes a cross with a surrounding arc, and mouse drag rotates the cut. This may look weird because the cut remains being a rectangle, and when  the horizontal and vertical physical resolutions (like pixels/mm) of the image do not match, atlas cut will appear stretching/shrinking with the rotation.
162
163 After each transformation step, marker resets to a cross (translation mode).
164
165 //Note!// The panel can be resized towards the left (common border with Control Panel) and towards the bottom (common border with Filmstrip).
166
167 4. Save the position by pressing //"Store". //The registration is copied to the remaining slides to help with scaling (visible also in the filmstrip)
168
169 5. Go through all sections and refine position and cutting angles.
170
171 //Note!// When jumping from one section to the other, wait a few seconds for the image to load
172
173 //Note!// The "restore" button allows you to go back to the saved position if necessary
174
175 6. Save your results in the descriptor file (json) by pressing "Save to bucket".
176
177 7. When the registration is finished, you can export your descriptor files ( .flat files used for analysis in the QUINT workflow) by pressing //"export overlays".//
178
179 **Control panel:**
180
181 |=Button|=Function
182 |Store |Store the current alignment and propagate to unaligned sections (**Note** this does not save the series to your bucket)
183 |Restore |Reset the current alignment to the last stored position
184 |Clear |Reset the current alignment to the default position
185 |Overlay Slider |Opacity of the atlas overlay, when fully opaque, it becomes an outline
186 |Overlay color |The outline color
187 |Filmstrip slider and color|The above settings, applied to the filmstrip
188 |Save to bucket|Save the series to your bucket (and overwrite the existing file)
189 |Export overlays|Generates a series of .flat files (for Nutil or similar utility), and stores them into a .zip file in the bucket (re-using the name of the series descriptor, e.g. series13.json will export series13.zip)
190
191
192 The right border of the control panel can be dragged horizontally, allowing to resize the panel and the main view
193
194 **Filmstrip:**
195
196 Drag horizontally to see series, click on a section in order to load it into the main view The top border of the filmstrip can be dragged vertically, allowing to resize the panel and the main view
197
198 **Navigation panel:**
199
200 Shows the three standard planes centered around the midpoint of the current alignment visible in the main view.
201
202 The rectangle of the current cut is projected on each standard plane as a yellow line/rectangle/parallelogram. A small yellow circle represents the midpoint of the projection.
203
204 Drag the midpoint around to move the cut.
205
206 Drag anywhere else to rotate the cut (inside the given standard plane, around the midpoint).
207
208 == **How to use WebWarp** ==
209
210 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.
211
212 Online user manual: [[https:~~/~~/webwarp.readthedocs.io/en/latest/>>https://webwarp.readthedocs.io/en/latest/]]
213
214 The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
215
216 === Opening a sample dataset ===
217
218 Demo dataset is loaded using the file: **demo_mouse_data.waln**
219
220 You can see the result of a finished anchoring by choosing the file: **demo_mouse_data.wwrp**
221
222 === Opening a private dataset ===
223
224 (% class="wikigeneratedid" %)
225 All the .waln files located in the Bucket are displayed on the WebWarp main page. Your progress in WebWarp is saved as a .wwrp file.
226
227 === Opening an EBRAINS dataset ===
228
229 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.
230
231 === Non-linear registration ===
232
233 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.
234 1. Select the waln file corresponding to your result from the WebAlign image registration.
235 1. Wait for the images to load: this may take some time.
236
237 [[~[~[image:image1.png~|~|alt="_images/image1.png"~]~]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
238
239 Your registered images are visible in the main window. The atlas regions with transparency sliders can be toggled using the “Atlas opacity” button. The color of the atlas outline can be modified by clicking on the colored rectangle.
240
241 4. When going to “Settings”, the button for selecting the marker color will appear as well as “show triangles” which correspond to areas affected by the same    transformation.
242
243 5. Place a marker on an area you want to stretch using the space bar. Nonlinear distortions are applied by dragging a marker using the mouse.
244
245 6. Press Delete or Backspace to remove a marker under the mouse cursor.
246
247 7. Save your results pression the “save” button. “Save as” will allow you to save the adjustments as a new file with a different name.
248
249 8. When the registration is finished, you can export your descriptor files ( .seg files used for analysis in the QUINT workflow) by pressing “export overlays”. All results are zipped and stored in the bucket. The result file name will be the same as the one chosen to create the registration, e.g. “my-registration.zip”.
250
251
252
253
254 == **How to use LocaliZoom** ==
255
256 LocaliZoom is a web application for viewing of series of high-resolution 2D images that have been anchored to reference atlases. LocaliZoom allows the viewing and exploring of high-resolution images with superimposed atlas overlays, and the extraction of coordinates of annotated points within those images for viewing in 3D brain atlas space.
257
258 Online Manual: [[https:~~/~~/localizoom.readthedocs.io/en/latest/>>https://localizoom.readthedocs.io/en/latest/]]
259
260 The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
261
262 === Opening a sample dataset ===
263
264 A demo dataset is loaded using the file: demo_mouse_data_lz
265
266 === Opening a private or EBRAINS dataset ===
267
268 LocaliZoom will open all WebAlign (.waln) or WebWarp (.wwrp) files.
269
270 === Create annotation points ===
271
272 To extract a coordinate, the mouse marker must be positioned at the desired location, and press the space bar. A cross will appear in the selected colour (under Settings), representing the location of the extracted coordinate. After all desired points have been marked, the coordinates can be exported either to Excel.
273
274 Press "delete" in order to remove an annotation.
275
276 Save your annotations with the "save" or "save as" buttons. The file format is .lz
277
278 === Export of coordinate points ===
279
280 The created points can be exported to an Excel book by pressing "XLSX export".
281
282 The saved .lz file can also be visualised in the 3D viewer, MeshView.
283
284 == **How to use MeshView** ==
285
286 MeshView is a web application for real-time 3D display of surface mesh data representing structural parcellations from volumetric atlases, and point clouds extracted from datasets.
287
288 Online manual: [[https:~~/~~/meshview-for-brain-atlases.readthedocs.io/en/latest>>https://meshview-for-brain-atlases.readthedocs.io/en/latest]]
289
290 The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
291
292 === Open point cloud files ===
293
294 MeshView can open annotations from LocaliZoom (.lz files). Possibility of a global control of all structures, using the slider will render the meshes transparent or disappear.
295
296 The individual control allow each structure to be made transparent or disappear. The color for each structure can be changed when clicking on the colored square.
297
298 Navigation in the hierarchy is possible by clicking on the region names (grey boxes), this will collapse parts of the region tree.
299
300 === Export images ===
301
302 The "screenshot" button allows to capture the main window view as a png file.
303
304 [[image:image19.png]]
305
306