Version 54.1 by puchades on 2025/02/13 10:00
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puchades 6.1 1 == To set up your working environment: ==
puchades 1.1 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.
puchades 53.1 5 1. Remember to set your data proxy bucket to "public". Your collab can still be private.
puchades 1.1 6 1. Give users Admin, Editor or Viewer rights by clicking** Team** in the navigation panel.
puchades 53.1 7 1. Install WebAlign, WebWarp, LocaliZoom, and Meshview from the EBRAINS Collaboratory App Store (see instructions below)[[image:public_data_proxy_bucket.png]]
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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.
puchades 10.1 14 1. Repeat this for all the relevant Community Apps. You will need, "QUINT Image creator app"; "WebAlign"; "WebWarp"; "LocaliZoom" and "MeshView".
puchades 1.1 15 1. Navigate between the Apps in the navigation panel. File transfer between the Apps is through the Bucket.
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puchades 8.2 17 == How to prepare your images? ==
puchades 2.1 18
19 **~1. Prepare your images before upload by naming them according this naming convention:**
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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).
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puchades 8.2 23 Example: tg2345_MMSH_s001.tif
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puchades 8.3 25 - Upload the images you want to work with into the bucket of your collab using the Data proxy (press on //"Bucket"//)
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puchades 8.2 27 **2. Image ingestion**
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puchades 54.1 29 Use the DeepZoom app
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puchades 19.1 33 Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
puchades 8.2 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.
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37 When the ingestion is finished, your serie will appear under the "Prepared Brains" tab.
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39 Click on the "View Brain" button in order to preview your images.
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puchades 24.1 41 Now go to the WebAlign app in order to start the registration to atlas.
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puchades 18.1 43 [[image:Screenshot create_brain app.png]]
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45
puchades 24.1 46 === Use Image service app (alt.) ===
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puchades 23.1 48 **2b. Start the Image service UI from your webapp**
puchades 8.3 49
puchades 23.1 50 * ** Fill in the requested information:**
puchades 8.3 51
52 - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
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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.
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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
puchades 54.1 64 [[~[~[image:Skjermbilde 2022-02-08 103443.png~|~|height="199" width="500"~]~]>>attach:Skjermbilde 2022-02-08 103443.png]]
puchades 8.3 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)
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puchades 22.1 68 [[image:create collab.png]]
puchades 8.3 69
70 - Customize your ingestion:
71
72 - give a name to your ingestion in the "description of ingestion" field.
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puchades 23.1 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**
puchades 8.3 78
79 Press "Task" in the higher right corner of the window.
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81 When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
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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"
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87 Refresh your browser in order to check the status of your task.
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89 When "successful", your chunks have been created.
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puchades 3.1 91 == **How to use WebAlign** ==
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puchades 5.1 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.
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puchades 8.1 95 Online user manual: [[https:~~/~~/webalign.readthedocs.io/en/latest/>>https://webalign.readthedocs.io/en/latest/]]
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puchades 3.1 97 The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
98
99 === Opening a sample dataset ===
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puchades 25.1 101 Demo dataset is loaded using the file: **demo_mouse_data_start.waln**
puchades 3.1 102
puchades 25.1 103 You can see the result of a finished anchoring by choosing the file: **demo_mouse_data.waln**
puchades 3.1 104
105 === Opening a private dataset ===
106
puchades 25.1 107 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.
puchades 3.1 108
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
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puchades 27.1 111 2. WebAlign will search for DZIP files and list those found.
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113 3. Enter a name for the descriptor json file which will be created and will contain your anchoring information.
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115 4. Choose the target 3D reference atlas (WHSv3 for Rat and CCFv3_2017 for Mouse).
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117 5. Press //"create"//. The main window will now display WebAlign. This step can take some time.
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puchades 27.1 119 [[image:create series webAlign.png]]
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puchades 33.1 121 === Opening an EBRAINS dataset ===
puchades 27.1 122
puchades 28.1 123 (% class="wikigeneratedid" %)
puchades 33.1 124 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.
puchades 28.1 125
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.
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puchades 3.1 129 === 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**
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143 The main window shows the selected image with the atlas overlay.
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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.
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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.
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151 3. The main window supports mouse drag in multiple modes in order to stretch the atlas and find the correct position.
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153 -If there is no marker, or the marker is a cross, mouse drag slides the cut in its plane (translation).
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155 -Keyboard controls to modify mouse drag (they also place the marker if it's not placed already):
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157 -Left/Right arrow keys: marker becomes a vertical line, and mouse drag horizontally resizes the cut
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159 -Up/Down arrow keys: marker becomes a horizontal line, and mouse drag vertically resizes the cut
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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.
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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).
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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)
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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
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173 //Note!// The "restore" button allows you to go back to the saved position if necessary
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175 6. Save your results in the descriptor file (json) by pressing "Save to bucket".
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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)
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191
192 The right border of the control panel can be dragged horizontally, allowing to resize the panel and the main view
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194 **Filmstrip:**
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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
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198 **Navigation panel:**
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200 Shows the three standard planes centered around the midpoint of the current alignment visible in the main view.
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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.
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204 Drag the midpoint around to move the cut.
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puchades 31.1 206 Drag anywhere else to rotate the cut (inside the given standard plane, around the midpoint).
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puchades 32.1 208 == **How to use WebWarp** ==
puchades 33.2 209
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.
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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**
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220 You can see the result of a finished anchoring by choosing the file: **demo_mouse_data.wwrp**
221
puchades 34.1 222 === Opening a private dataset ===
223
puchades 39.2 224 (% 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 ===
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puchades 34.1 233 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.
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puchades 54.1 237 [[~[~[image:image1.png~|~|alt="_images/image1.png"~]~]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
puchades 34.1 238
puchades 39.2 239 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.
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puchades 40.1 241 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.
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puchades 39.2 243 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.
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245 6. Press Delete or Backspace to remove a marker under the mouse cursor.
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puchades 40.1 247 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.
puchades 39.2 248
puchades 40.1 249 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”.
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253
puchades 34.2 254 == **How to use LocaliZoom** ==
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puchades 36.1 256 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.
puchades 34.2 257
puchades 36.1 258 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
puchades 41.2 266 === Opening a private or EBRAINS dataset ===
puchades 36.1 267
puchades 41.2 268 LocaliZoom will open all WebAlign (.waln) or WebWarp (.wwrp) files.
puchades 36.1 269
puchades 41.2 270 === Create annotation points ===
puchades 35.1 271
puchades 42.1 272 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.
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puchades 42.1 274 Press "delete" in order to remove an annotation.
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puchades 42.1 276 Save your annotations with the "save" or "save as" buttons. The file format is .lz
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puchades 41.2 278 === Export of coordinate points ===
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puchades 42.1 280 The created points can be exported to an Excel book by pressing "XLSX export".
puchades 41.2 281
puchades 42.2 282 The saved .lz file can also be visualised in the 3D viewer, MeshView.
puchades 42.1 283
puchades 37.1 284 == **How to use MeshView** ==
puchades 35.1 285
puchades 44.1 286 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.
puchades 35.1 287
puchades 44.1 288 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 ===
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puchades 49.1 294 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.
puchades 44.1 295
puchades 50.1 296 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.
puchades 49.1 297
298 Navigation in the hierarchy is possible by clicking on the region names (grey boxes), this will collapse parts of the region tree.
299
puchades 48.1 300 === Export images ===
301
puchades 47.1 302 The "screenshot" button allows to capture the main window view as a png file.
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puchades 46.1 304 [[image:image19.png]]
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