Last modified by puchades on 2025/02/13 10:43
From version 64.1
edited by puchades
on 2025/02/13 10:43
Change comment: There is no comment for this version
To version 9.1
edited by puchades
on 2023/06/21 10:19
Change comment: There is no comment for this version

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2 2  
3 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 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 6  1. Give users Admin, Editor or Viewer rights by clicking** Team** in the navigation panel.
7 -1. Install DeepZoom, WebAlign, WebWarp, LocaliZoom, and Meshview from the EBRAINS Collaboratory App Store (see instructions below)[[image:public_data_proxy_bucket.png]]
6 +1. Install WebAlign, LocaliZoom, and Meshview from the EBRAINS Collaboratory App Store (see instructions below)
8 8  
9 9  == How to install Collaboratory Apps ==
10 10  
11 11  1. To install Collaboratory Apps, click on the + Create button (top right corner).
12 -1. Give the page a Title (for example, DeepZoom), select the Community App option, and click Create.
13 -1. Select the App to install (for example, DeepZoom), and click Save and View.
14 -1. Repeat this for all the relevant Community Apps. You will need, "DeepZoom"; "WebAlign"; "WebWarp"; "LocaliZoom" and "MeshView".
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.
13 +1. Repeat this for all the relevant Community Apps.
15 15  1. Navigate between the Apps in the navigation panel. File transfer between the Apps is through the Bucket.
16 16  
17 -[[image:1739438141762-762.png||height="414" width="300"]]
18 -
19 19  == How to prepare your images? ==
20 20  
21 21  **~1. Prepare your images before upload by naming them according this naming convention:**
... ... @@ -28,243 +28,287 @@
28 28  
29 29  **2. Image ingestion**
30 30  
31 -Open the DeepZoom app and login with your EBRAINS credentials.
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:
32 32  
30 +(% class="wikigeneratedid" %)
31 +=== ===
33 33  
33 +=== Use the "QUINT image creator" app ===
34 34  
35 -[[image:Screenshot 2025-02-13 101940.png]]
35 +**~1. 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.
37 37  
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.
38 38  
41 +When the ingestion is finished, your serie will appear under the "Prepared Brains" tab.
39 39  
40 -Select your bucket, the one where your images are stored.
43 +Click on the "View Brain" button in order to preview your images.
41 41  
42 -Select the appropriate folder and click "Browse source" in order to visualise the images to ingest.
43 43  
44 -Enter the URL of the bucket by typing "/bucket_name/output_folder_name"
45 45  
46 -Press "Start process".
47 47  
48 -By refreshing the status, you will see when the ingestion is completed.
48 +== ==
49 49  
50 -You now will have pyramid files in DZI format in your output folder. These can be opened by the WebAlign app.
50 +=== Use Image service app ===
51 51  
52 +**~1. Start the Image service UI from your webapp**
52 52  
53 -[[image:1739439061155-890.png]]
54 +**2. Fill in the requested information:**
54 54  
55 -== **How to use WebAlign** ==
56 + - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
56 56  
57 -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.
58 +E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
58 58  
59 -Online user manual: [[https:~~/~~/webalign.readthedocs.io/en/latest/>>https://webalign.readthedocs.io/en/latest/]]
60 + - 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.
60 60  
61 -The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
62 + - 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"
62 62  
63 -=== Opening a sample dataset ===
64 + - Or use a prefix: E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab?prefix=name_of_the_data_folder
64 64  
65 -Demo dataset is loaded using the file: **demo_mouse_data_start.waln**
66 + - allow the image service to access your bucket
66 66  
67 -You can see the result of a finished anchoring by choosing the file: **demo_mouse_data.waln**
68 +[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]
68 68  
69 -=== Opening a private dataset ===
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)
70 70  
71 -After you have uploaded your images to the bucket and ingested your images with the DeepZoom app, this has generated DZIP chunks. These DZIP files are used by WebAlign.
72 +[[image:create collab.png||height="427" width="900"]]
72 72  
73 -~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
74 +- Customize your ingestion:
74 74  
75 -2. WebAlign will search for DZIP files and list those found.
76 + - give a name to your ingestion in the "description of ingestion" field.
76 76  
77 -3. Enter a name for the descriptor json file which will be created and will contain your anchoring information.
78 +**3. For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
78 78  
79 -4. Choose the target 3D reference atlas (WHSv3 for Rat and CCFv3_2017 for Mouse).
80 +**4. Click //"preview"// in order to preview your task**
80 80  
81 -5. Press //"create"//. The main window will now display WebAlign. This step can take some time.
82 +**5. Click //"create task"//  to launch your ingestion**
82 82  
83 -[[image:create series webAlign.png]]
84 +**6. Checking results in the Main UI page**
84 84  
85 -=== Opening an EBRAINS dataset ===
86 +Press "Task" in the higher right corner of the window.
86 86  
87 -(% class="wikigeneratedid" %)
88 -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.
88 +When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
89 89  
90 -(% class="wikigeneratedid" %)
91 -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.
90 +Otherwise, you will be redirected to the tasks list where the created task is selected.
92 92  
93 -=== Registration instructions ===
92 +//Note! //A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"
94 94  
95 -**Short keys**
94 +Refresh your browser in order to check the status of your task.
96 96  
97 -|=To do this|=Press|=Description
98 -|Place marker|Space bar|Markers are the anchor points of most transformations (stretch and rotate).
99 -|Remove marker|Esc|Removes a previously placed marker.
100 -|Horizontal stretch from marker |Left/Right arrow keys|Marker becomes a vertical line, and mouse drag horizontally resizes the cut.
101 -|Vertical stretch from marker |Up/Down arrow keys|Marker becomes a horizontal line, and mouse drag vertically resizes the cut
102 -|Rotate around marker|PgUp/PgDown|Marker becomes a cross with a surrounding arc, and mouse drag rotates the cut.
103 -|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).
96 +When "successful", your chunks have been created.
104 104  
105 -**Start the registration**
98 +== ==
106 106  
107 -The main window shows the selected image with the atlas overlay.
100 +=== Use Image service app ===
108 108  
109 --If necessary, change the atlas from coronal view to sagittal or horizontal view (see Navigation panel below)
102 +**~1. Start the Image service UI from your webapp**
110 110  
111 -~1. Move the atlas to the approximate position of your section using the yellow dots in the three small windows from the navigation panel.
104 +**2. Fill in the requested information:**
112 112  
113 -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.
106 + - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
114 114  
115 -3. The main window supports mouse drag in multiple modes in order to stretch the atlas and find the correct position.
108 +E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
116 116  
117 --If there is no marker, or the marker is a cross, mouse drag slides the cut in its plane (translation).
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.
118 118  
119 --Keyboard controls to modify mouse drag (they also place the marker if it's not placed already):
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"
120 120  
121 - -Left/Right arrow keys: marker becomes a vertical line, and mouse drag horizontally resizes the cut
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
122 122  
123 - -Up/Down arrow keys: marker becomes a horizontal line, and mouse drag vertically resizes the cut
116 + - allow the image service to access your bucket
124 124  
125 - -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.
118 +[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]
126 126  
127 -After each transformation step, marker resets to a cross (translation mode).
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)
128 128  
129 - //Note!// The panel can be resized towards the left (common border with Control Panel) and towards the bottom (common border with Filmstrip).
122 +[[image:create collab.png||height="427" width="900"]]
130 130  
131 -4. Save the position by pressing //"Store". //The registration is copied to the remaining slides to help with scaling (visible also in the filmstrip)
124 +- Customize your ingestion:
132 132  
133 -5. Go through all sections and refine position and cutting angles.
126 + - give a name to your ingestion in the "description of ingestion" field.
134 134  
135 - //Note!// When jumping from one section to the other, wait a few seconds for the image to load
128 +**3. For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
136 136  
137 - //Note!// The "restore" button allows you to go back to the saved position if necessary
130 +**4. Click //"preview"// in order to preview your task**
138 138  
139 -6. Save your results in the descriptor file (json) by pressing "Save to bucket".
132 +**5. Click //"create task"//  to launch your ingestion**
140 140  
141 -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".//
134 +**6. Checking results in the Main UI page**
142 142  
143 -**Control panel:**
136 +Press "Task" in the higher right corner of the window.
144 144  
145 -|=Button|=Function
146 -|Store |Store the current alignment and propagate to unaligned sections (**Note** this does not save the series to your bucket)
147 -|Restore |Reset the current alignment to the last stored position
148 -|Clear |Reset the current alignment to the default position
149 -|Overlay Slider |Opacity of the atlas overlay, when fully opaque, it becomes an outline
150 -|Overlay color |The outline color
151 -|Filmstrip slider and color|The above settings, applied to the filmstrip
152 -|Save to bucket|Save the series to your bucket (and overwrite the existing file)
153 -|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)
154 -
138 +When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
155 155  
156 -The right border of the control panel can be dragged horizontally, allowing to resize the panel and the main view
140 +Otherwise, you will be redirected to the tasks list where the created task is selected.
157 157  
158 -**Filmstrip:**
142 +//Note! //A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"
159 159  
160 -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
144 +Refresh your browser in order to check the status of your task.
161 161  
162 -**Navigation panel:**
146 +When "successful", your chunks have been created.
163 163  
164 -Shows the three standard planes centered around the midpoint of the current alignment visible in the main view.
148 +== ==
165 165  
166 -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.
150 +=== Use Image service app ===
167 167  
168 -Drag the midpoint around to move the cut.
152 +**~1. Prepare your images before upload by naming them according this naming convention:**
169 169  
170 -Drag anywhere else to rotate the cut (inside the given standard plane, around the midpoint).
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).
171 171  
172 -== **How to use WebWarp** ==
156 +Example: tg2345_MMSH_s001_segmentation.png
173 173  
174 -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.
158 +- Upload the images you want to work with into the bucket of your collab using the Data proxy (press on //"Bucket"//)
175 175  
176 -Online user manual: [[https:~~/~~/webwarp.readthedocs.io/en/latest/>>https://webwarp.readthedocs.io/en/latest/]]
160 +**2. Start the Image service UI from your webapp**
177 177  
178 -The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
162 +**3. Fill in the requested information:**
179 179  
180 -=== Opening a sample dataset ===
164 + - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
181 181  
182 -Demo dataset is loaded using the file: **demo_mouse_data.waln**
166 +E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
183 183  
184 -You can see the result of a finished anchoring by choosing the file: **demo_mouse_data.wwrp**
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.
185 185  
186 -=== Opening a private dataset ===
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"
187 187  
188 -(% class="wikigeneratedid" %)
189 -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.
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
190 190  
191 -=== Opening an EBRAINS dataset ===
174 + - allow the image service to access your bucket
192 192  
193 -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.
176 +[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]
194 194  
195 -=== Non-linear registration ===
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)
196 196  
197 -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.
198 -1. Select the waln file corresponding to your result from the WebAlign image registration.
199 -1. Wait for the images to load: this may take some time.
180 +[[image:create collab.png||height="427" width="900"]]
200 200  
201 -[[~[~[image:image1.png~|~|alt="_images/image1.png"~]~]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
182 +- Customize your ingestion:
202 202  
203 -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.
184 + - give a name to your ingestion in the "description of ingestion" field.
204 204  
205 - 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.
186 +**3. For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
206 206  
207 - 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.
188 +**4. Click //"preview"// in order to preview your task**
208 208  
209 - 6. Press Delete or Backspace to remove a marker under the mouse cursor.
190 +**5. Click //"create task"//  to launch your ingestion**
210 210  
211 - 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.
192 +**6. Checking results in the Main UI page**
212 212  
213 - 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”.
194 +Press "Task" in the higher right corner of the window.
214 214  
196 +When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
215 215  
216 -
198 +Otherwise, you will be redirected to the tasks list where the created task is selected.
217 217  
218 -== **How to use LocaliZoom** ==
200 +//Note! //A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"
219 219  
220 -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.
202 +Refresh your browser in order to check the status of your task.
221 221  
222 -Online Manual: [[https:~~/~~/localizoom.readthedocs.io/en/latest/>>https://localizoom.readthedocs.io/en/latest/]]
204 +When "successful", your chunks have been created.
223 223  
206 +== **How to use WebAlign** ==
207 +
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.
209 +
210 +Online user manual: [[https:~~/~~/webalign.readthedocs.io/en/latest/>>https://webalign.readthedocs.io/en/latest/]]
211 +
224 224  The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
225 225  
226 226  === Opening a sample dataset ===
227 227  
228 - A demo dataset is loaded using the file: demo_mouse_data_lz
216 +Demo dataset is loaded using the file: **demo_mouse_data_start**
229 229  
230 -=== Opening a private or EBRAINS dataset ===
218 +You can see the result of a finished anchoring by choosing the file: **demo_mouse_data**
231 231  
232 -LocaliZoom will open all WebAlign (.waln) or WebWarp (.wwrp) files.
220 +=== Opening a private dataset ===
233 233  
234 -=== Create annotation points ===
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.
235 235  
236 -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.
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
237 237  
238 -Press "delete" in order to remove an annotation.
226 +2. WebAlign will search for DZI files and list those found.
239 239  
240 -Save your annotations with the "save" or "save as" buttons. The file format is .lz
228 +3. Enter a name for the descriptor json file which will be created and will contain your anchoring information.
241 241  
242 -=== Export of coordinate points ===
230 +4. Choose the target 3D reference atlas (WHSv3 for Rat and CCFv3_2017 for Mouse).
243 243  
244 -The created points can be exported to an Excel book by pressing "XLSX export".
232 +5. Press //"create"//. The main window will now display WebAlign. This step can take some time.
245 245  
246 -The saved .lz file can also be visualised in the 3D viewer, MeshView.
234 +=== Registration instructions ===
247 247  
248 -== **How to use MeshView** ==
236 +**Short keys**
249 249  
250 -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.
238 +|=To do this|=Press|=Description
239 +|Place marker|Space bar|Markers are the anchor points of most transformations (stretch and rotate).
240 +|Remove marker|Esc|Removes a previously placed marker.
241 +|Horizontal stretch from marker |Left/Right arrow keys|Marker becomes a vertical line, and mouse drag horizontally resizes the cut.
242 +|Vertical stretch from marker |Up/Down arrow keys|Marker becomes a horizontal line, and mouse drag vertically resizes the cut
243 +|Rotate around marker|PgUp/PgDown|Marker becomes a cross with a surrounding arc, and mouse drag rotates the cut.
244 +|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).
251 251  
252 -Online manual: [[https:~~/~~/meshview-for-brain-atlases.readthedocs.io/en/latest>>https://meshview-for-brain-atlases.readthedocs.io/en/latest]]
246 +**Start the registration**
253 253  
254 -The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
248 +The main window shows the selected image with the atlas overlay.
255 255  
256 -=== Open point cloud files ===
250 +-If necessary, change the atlas from coronal view to sagittal or horizontal view (see Navigation panel below)
257 257  
258 -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.
252 +~1. Move the atlas to the approximate position of your section using the yellow dots in the three small windows from the navigation panel.
259 259  
260 -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.
254 +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.
261 261  
262 -Navigation in the hierarchy is possible by clicking on the region names (grey boxes), this will collapse parts of the region tree.
256 +3. The main window supports mouse drag in multiple modes in order to stretch the atlas and find the correct position.
263 263  
264 -=== Export images ===
258 +-If there is no marker, or the marker is a cross, mouse drag slides the cut in its plane (translation).
265 265  
266 -The "screenshot" button allows to capture the main window view as a png file.
260 +-Keyboard controls to modify mouse drag (they also place the marker if it's not placed already):
267 267  
268 -[[image:image19.png]]
262 + -Left/Right arrow keys: marker becomes a vertical line, and mouse drag horizontally resizes the cut
269 269  
264 + -Up/Down arrow keys: marker becomes a horizontal line, and mouse drag vertically resizes the cut
265 +
266 + -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.
267 +
268 +After each transformation step, marker resets to a cross (translation mode).
269 +
270 + //Note!// The panel can be resized towards the left (common border with Control Panel) and towards the bottom (common border with Filmstrip).
271 +
272 +4. Save the position by pressing //"Store". //The registration is copied to the remaining slides to help with scaling (visible also in the filmstrip)
273 +
274 +5. Go through all sections and refine position and cutting angles.
275 +
276 + //Note!// When jumping from one section to the other, wait a few seconds for the image to load
277 +
278 + //Note!// The "restore" button allows you to go back to the saved position if necessary
279 +
280 +6. Save your results in the descriptor file (json) by pressing "Save to bucket".
281 +
282 +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".//
283 +
284 +**Control panel:**
285 +
286 +|=Button|=Function
287 +|Store |Store the current alignment and propagate to unaligned sections (**Note** this does not save the series to your bucket)
288 +|Restore |Reset the current alignment to the last stored position
289 +|Clear |Reset the current alignment to the default position
290 +|Overlay Slider |Opacity of the atlas overlay, when fully opaque, it becomes an outline
291 +|Overlay color |The outline color
292 +|Filmstrip slider and color|The above settings, applied to the filmstrip
293 +|Save to bucket|Save the series to your bucket (and overwrite the existing file)
294 +|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)
270 270  
296 +
297 +The right border of the control panel can be dragged horizontally, allowing to resize the panel and the main view
298 +
299 +**Filmstrip:**
300 +
301 +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
302 +
303 +**Navigation panel:**
304 +
305 +Shows the three standard planes centered around the midpoint of the current alignment visible in the main view.
306 +
307 +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.
308 +
309 +Drag the midpoint around to move the cut.
310 +
311 +Drag anywhere else to rotate the cut (inside the given standard plane, around the midpoint)
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