Version 12.1 by puchades on 2023/06/21 10:23
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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.
5 1. Give users Admin, Editor or Viewer rights by clicking** Team** in the navigation panel.
6 1. Install WebAlign, LocaliZoom, and Meshview from the EBRAINS Collaboratory App Store (see instructions below)
7
8 == How to install Collaboratory Apps ==
9
10 1. To install Collaboratory Apps, click on the + Create button (top right corner).
11 1. Give the page a Title (for example, WebAlign), select the Community App option, and click Create.
12 1. Select the App to install (for example, WebAlign), and click Save and View.
puchades 10.1 13 1. Repeat this for all the relevant Community Apps. You will need, "QUINT Image creator app"; "WebAlign"; "WebWarp"; "LocaliZoom" and "MeshView".
puchades 1.1 14 1. Navigate between the Apps in the navigation panel. File transfer between the Apps is through the Bucket.
15
puchades 8.2 16 == How to prepare your images? ==
puchades 2.1 17
18 **~1. Prepare your images before upload by naming them according this naming convention:**
19
20 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).
21
puchades 8.2 22 Example: tg2345_MMSH_s001.tif
23
puchades 8.3 24 - Upload the images you want to work with into the bucket of your collab using the Data proxy (press on //"Bucket"//)
25
puchades 8.2 26 **2. Image ingestion**
27
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
30 === Use the "QUINT image creator" app ===
31
32 **~1. Select images to ingest**
33
34 Shift-Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
35
36 The App will automatically generate the files for you. Monitor the progress under the "processing" tab and on the two dashboards on the left.
37
38 When the ingestion is finished, your serie will appear under the "Prepared Brains" tab.
39
40 Click on the "View Brain" button in order to preview your images.
41
42
puchades 12.1 43
puchades 8.2 44
45 == ==
46
47 === Use Image service app ===
48
puchades 8.3 49 **~1. Start the Image service UI from your webapp**
50
51 **2. Fill in the requested information:**
52
53 - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
54
55 E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
56
57 - 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.
58
59 - 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"
60
61 - Or use a prefix: E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab?prefix=name_of_the_data_folder
62
63 - allow the image service to access your bucket
64
65 [[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]
66
67 - 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)
68
69 [[image:create collab.png||height="427" width="900"]]
70
71 - Customize your ingestion:
72
73 - give a name to your ingestion in the "description of ingestion" field.
74
75 **3. For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
76
77 **4. Click //"preview"// in order to preview your task**
78
79 **5. Click //"create task"//  to launch your ingestion**
80
81 **6. Checking results in the Main UI page**
82
83 Press "Task" in the higher right corner of the window.
84
85 When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
86
87 Otherwise, you will be redirected to the tasks list where the created task is selected.
88
89 //Note! //A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"
90
91 Refresh your browser in order to check the status of your task.
92
93 When "successful", your chunks have been created.
94
95 == ==
96
puchades 11.1 97
puchades 8.3 98
puchades 9.1 99 [[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]
100
101 - 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)
102
103 [[image:create collab.png||height="427" width="900"]]
104
105 - Customize your ingestion:
106
107 - give a name to your ingestion in the "description of ingestion" field.
108
109 **3. For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
110
111 **4. Click //"preview"// in order to preview your task**
112
113 **5. Click //"create task"//  to launch your ingestion**
114
115 **6. Checking results in the Main UI page**
116
117 Press "Task" in the higher right corner of the window.
118
119 When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
120
121 Otherwise, you will be redirected to the tasks list where the created task is selected.
122
123 //Note! //A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"
124
125 Refresh your browser in order to check the status of your task.
126
127 When "successful", your chunks have been created.
128
129 == ==
130
131 === Use Image service app ===
132
puchades 8.2 133 **~1. Prepare your images before upload by naming them according this naming convention:**
134
135 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).
136
puchades 2.1 137 Example: tg2345_MMSH_s001_segmentation.png
138
139 - Upload the images you want to work with into the bucket of your collab using the Data proxy (press on //"Bucket"//)
140
141 **2. Start the Image service UI from your webapp**
142
143 **3. Fill in the requested information:**
144
145 - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
146
puchades 7.1 147 E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
puchades 2.1 148
puchades 7.1 149 - 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.
puchades 2.1 150
151 - 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"
152
puchades 7.1 153 - Or use a prefix: E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab?prefix=name_of_the_data_folder
puchades 2.1 154
155 - allow the image service to access your bucket
156
157 [[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]
158
159 - 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)
160
161 [[image:create collab.png||height="427" width="900"]]
162
163 - Customize your ingestion:
164
165 - give a name to your ingestion in the "description of ingestion" field.
166
167 **3. For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
168
169 **4. Click //"preview"// in order to preview your task**
170
171 **5. Click //"create task"//  to launch your ingestion**
172
173 **6. Checking results in the Main UI page**
174
175 Press "Task" in the higher right corner of the window.
176
177 When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
178
179 Otherwise, you will be redirected to the tasks list where the created task is selected.
180
181 //Note! //A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"
182
183 Refresh your browser in order to check the status of your task.
184
185 When "successful", your chunks have been created.
puchades 3.1 186
187 == **How to use WebAlign** ==
188
puchades 5.1 189 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.
190
puchades 8.1 191 Online user manual: [[https:~~/~~/webalign.readthedocs.io/en/latest/>>https://webalign.readthedocs.io/en/latest/]]
192
puchades 3.1 193 The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
194
195 === Opening a sample dataset ===
196
puchades 5.1 197 Demo dataset is loaded using the file: **demo_mouse_data_start**
puchades 3.1 198
199 You can see the result of a finished anchoring by choosing the file: **demo_mouse_data**
200
201 === Opening a private dataset ===
202
203 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.
204
205 ~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
206
207 2. WebAlign will search for DZI files and list those found.
208
209 3. Enter a name for the descriptor json file which will be created and will contain your anchoring information.
210
211 4. Choose the target 3D reference atlas (WHSv3 for Rat and CCFv3_2017 for Mouse).
212
213 5. Press //"create"//. The main window will now display WebAlign. This step can take some time.
214
215 === Registration instructions ===
216
217 **Short keys**
218
219 |=To do this|=Press|=Description
220 |Place marker|Space bar|Markers are the anchor points of most transformations (stretch and rotate).
221 |Remove marker|Esc|Removes a previously placed marker.
222 |Horizontal stretch from marker |Left/Right arrow keys|Marker becomes a vertical line, and mouse drag horizontally resizes the cut.
223 |Vertical stretch from marker |Up/Down arrow keys|Marker becomes a horizontal line, and mouse drag vertically resizes the cut
224 |Rotate around marker|PgUp/PgDown|Marker becomes a cross with a surrounding arc, and mouse drag rotates the cut.
225 |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).
226
227 **Start the registration**
228
229 The main window shows the selected image with the atlas overlay.
230
231 -If necessary, change the atlas from coronal view to sagittal or horizontal view (see Navigation panel below)
232
233 ~1. Move the atlas to the approximate position of your section using the yellow dots in the three small windows from the navigation panel.
234
235 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.
236
237 3. The main window supports mouse drag in multiple modes in order to stretch the atlas and find the correct position.
238
239 -If there is no marker, or the marker is a cross, mouse drag slides the cut in its plane (translation).
240
241 -Keyboard controls to modify mouse drag (they also place the marker if it's not placed already):
242
243 -Left/Right arrow keys: marker becomes a vertical line, and mouse drag horizontally resizes the cut
244
245 -Up/Down arrow keys: marker becomes a horizontal line, and mouse drag vertically resizes the cut
246
247 -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.
248
249 After each transformation step, marker resets to a cross (translation mode).
250
251 //Note!// The panel can be resized towards the left (common border with Control Panel) and towards the bottom (common border with Filmstrip).
252
253 4. Save the position by pressing //"Store". //The registration is copied to the remaining slides to help with scaling (visible also in the filmstrip)
254
255 5. Go through all sections and refine position and cutting angles.
256
257 //Note!// When jumping from one section to the other, wait a few seconds for the image to load
258
259 //Note!// The "restore" button allows you to go back to the saved position if necessary
260
261 6. Save your results in the descriptor file (json) by pressing "Save to bucket".
262
263 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".//
264
265 **Control panel:**
266
267 |=Button|=Function
268 |Store |Store the current alignment and propagate to unaligned sections (**Note** this does not save the series to your bucket)
269 |Restore |Reset the current alignment to the last stored position
270 |Clear |Reset the current alignment to the default position
271 |Overlay Slider |Opacity of the atlas overlay, when fully opaque, it becomes an outline
272 |Overlay color |The outline color
273 |Filmstrip slider and color|The above settings, applied to the filmstrip
274 |Save to bucket|Save the series to your bucket (and overwrite the existing file)
275 |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)
276
277
278 The right border of the control panel can be dragged horizontally, allowing to resize the panel and the main view
279
280 **Filmstrip:**
281
282 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
283
284 **Navigation panel:**
285
286 Shows the three standard planes centered around the midpoint of the current alignment visible in the main view.
287
288 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.
289
290 Drag the midpoint around to move the cut.
291
292 Drag anywhere else to rotate the cut (inside the given standard plane, around the midpoint)