Last modified by puchades on 2025/02/13 10:43
From version 58.1
edited by puchades
on 2025/02/13 10:15
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 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, 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".
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]]
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:**
... ... @@ -28,10 +28,17 @@
28 28  
29 29  **2. Image ingestion**
30 30  
31 -Use the DeepZoom app
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  
33 -Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
30 +(% class="wikigeneratedid" %)
31 +=== ===
34 34  
33 +=== Use the "QUINT image creator" app ===
34 +
35 +**~1. Select images to ingest**
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.
38 +
35 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 36  
37 37  When the ingestion is finished, your serie will appear under the "Prepared Brains" tab.
... ... @@ -38,227 +38,270 @@
38 38  
39 39  Click on the "View Brain" button in order to preview your images.
40 40  
41 -Now go to the WebAlign app in order to start the registration to atlas.
42 42  
43 43  
44 44  
45 -
48 +== ==
46 46  
47 -
50 +=== Use Image service app ===
48 48  
49 -== **How to use WebAlign** ==
52 +**~1. Start the Image service UI from your webapp**
50 50  
51 -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.
54 +**2. Fill in the requested information:**
52 52  
53 -Online user manual: [[https:~~/~~/webalign.readthedocs.io/en/latest/>>https://webalign.readthedocs.io/en/latest/]]
56 + - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
54 54  
55 -The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
58 +E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
56 56  
57 -=== Opening a sample dataset ===
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.
58 58  
59 -Demo dataset is loaded using the file: **demo_mouse_data_start.waln**
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"
60 60  
61 -You can see the result of a finished anchoring by choosing the file: **demo_mouse_data.waln**
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
62 62  
63 -=== Opening a private dataset ===
66 + - allow the image service to access your bucket
64 64  
65 -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.
68 +[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]
66 66  
67 -~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
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)
68 68  
69 -2. WebAlign will search for DZIP files and list those found.
72 +[[image:create collab.png||height="427" width="900"]]
70 70  
71 -3. Enter a name for the descriptor json file which will be created and will contain your anchoring information.
74 +- Customize your ingestion:
72 72  
73 -4. Choose the target 3D reference atlas (WHSv3 for Rat and CCFv3_2017 for Mouse).
76 + - give a name to your ingestion in the "description of ingestion" field.
74 74  
75 -5. Press //"create"//. The main window will now display WebAlign. This step can take some time.
78 +**3. For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
76 76  
77 -[[image:create series webAlign.png]]
80 +**4. Click //"preview"// in order to preview your task**
78 78  
79 -=== Opening an EBRAINS dataset ===
82 +**5. Click //"create task"//  to launch your ingestion**
80 80  
81 -(% class="wikigeneratedid" %)
82 -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.
84 +**6. Checking results in the Main UI page**
83 83  
84 -(% class="wikigeneratedid" %)
85 -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.
86 +Press "Task" in the higher right corner of the window.
86 86  
87 -=== Registration instructions ===
88 +When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
88 88  
89 -**Short keys**
90 +Otherwise, you will be redirected to the tasks list where the created task is selected.
90 90  
91 -|=To do this|=Press|=Description
92 -|Place marker|Space bar|Markers are the anchor points of most transformations (stretch and rotate).
93 -|Remove marker|Esc|Removes a previously placed marker.
94 -|Horizontal stretch from marker |Left/Right arrow keys|Marker becomes a vertical line, and mouse drag horizontally resizes the cut.
95 -|Vertical stretch from marker |Up/Down arrow keys|Marker becomes a horizontal line, and mouse drag vertically resizes the cut
96 -|Rotate around marker|PgUp/PgDown|Marker becomes a cross with a surrounding arc, and mouse drag rotates the cut.
97 -|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).
92 +//Note! //A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"
98 98  
99 -**Start the registration**
94 +Refresh your browser in order to check the status of your task.
100 100  
101 -The main window shows the selected image with the atlas overlay.
96 +When "successful", your chunks have been created.
102 102  
103 --If necessary, change the atlas from coronal view to sagittal or horizontal view (see Navigation panel below)
98 +== ==
104 104  
105 -~1. Move the atlas to the approximate position of your section using the yellow dots in the three small windows from the navigation panel.
100 +=== Use Image service app ===
106 106  
107 -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.
102 +**~1. Start the Image service UI from your webapp**
108 108  
109 -3. The main window supports mouse drag in multiple modes in order to stretch the atlas and find the correct position.
104 +**2. Fill in the requested information:**
110 110  
111 --If there is no marker, or the marker is a cross, mouse drag slides the cut in its plane (translation).
106 + - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
112 112  
113 --Keyboard controls to modify mouse drag (they also place the marker if it's not placed already):
108 +E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
114 114  
115 - -Left/Right arrow keys: marker becomes a vertical line, and mouse drag horizontally resizes the cut
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.
116 116  
117 - -Up/Down arrow keys: marker becomes a horizontal line, and mouse drag vertically resizes the cut
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"
118 118  
119 - -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.
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
120 120  
121 -After each transformation step, marker resets to a cross (translation mode).
116 + - allow the image service to access your bucket
122 122  
123 - //Note!// The panel can be resized towards the left (common border with Control Panel) and towards the bottom (common border with Filmstrip).
118 +[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]
124 124  
125 -4. Save the position by pressing //"Store". //The registration is copied to the remaining slides to help with scaling (visible also in the filmstrip)
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)
126 126  
127 -5. Go through all sections and refine position and cutting angles.
122 +[[image:create collab.png||height="427" width="900"]]
128 128  
129 - //Note!// When jumping from one section to the other, wait a few seconds for the image to load
124 +- Customize your ingestion:
130 130  
131 - //Note!// The "restore" button allows you to go back to the saved position if necessary
126 + - give a name to your ingestion in the "description of ingestion" field.
132 132  
133 -6. Save your results in the descriptor file (json) by pressing "Save to bucket".
128 +**3. For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
134 134  
135 -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".//
130 +**4. Click //"preview"// in order to preview your task**
136 136  
137 -**Control panel:**
132 +**5. Click //"create task"//  to launch your ingestion**
138 138  
139 -|=Button|=Function
140 -|Store |Store the current alignment and propagate to unaligned sections (**Note** this does not save the series to your bucket)
141 -|Restore |Reset the current alignment to the last stored position
142 -|Clear |Reset the current alignment to the default position
143 -|Overlay Slider |Opacity of the atlas overlay, when fully opaque, it becomes an outline
144 -|Overlay color |The outline color
145 -|Filmstrip slider and color|The above settings, applied to the filmstrip
146 -|Save to bucket|Save the series to your bucket (and overwrite the existing file)
147 -|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)
148 -
134 +**6. Checking results in the Main UI page**
149 149  
150 -The right border of the control panel can be dragged horizontally, allowing to resize the panel and the main view
136 +Press "Task" in the higher right corner of the window.
151 151  
152 -**Filmstrip:**
138 +When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
153 153  
154 -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
140 +Otherwise, you will be redirected to the tasks list where the created task is selected.
155 155  
156 -**Navigation panel:**
142 +//Note! //A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"
157 157  
158 -Shows the three standard planes centered around the midpoint of the current alignment visible in the main view.
144 +Refresh your browser in order to check the status of your task.
159 159  
160 -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.
146 +When "successful", your chunks have been created.
161 161  
162 -Drag the midpoint around to move the cut.
148 +== ==
163 163  
164 -Drag anywhere else to rotate the cut (inside the given standard plane, around the midpoint).
150 +=== Use Image service app ===
165 165  
166 -== **How to use WebWarp** ==
152 +**~1. Prepare your images before upload by naming them according this naming convention:**
167 167  
168 -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.
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).
169 169  
170 -Online user manual: [[https:~~/~~/webwarp.readthedocs.io/en/latest/>>https://webwarp.readthedocs.io/en/latest/]]
156 +Example: tg2345_MMSH_s001_segmentation.png
171 171  
172 -The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
158 +- Upload the images you want to work with into the bucket of your collab using the Data proxy (press on //"Bucket"//)
173 173  
174 -=== Opening a sample dataset ===
160 +**2. Start the Image service UI from your webapp**
175 175  
176 -Demo dataset is loaded using the file: **demo_mouse_data.waln**
162 +**3. Fill in the requested information:**
177 177  
178 -You can see the result of a finished anchoring by choosing the file: **demo_mouse_data.wwrp**
164 + - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
179 179  
180 -=== Opening a private dataset ===
166 +E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
181 181  
182 -(% class="wikigeneratedid" %)
183 -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.
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.
184 184  
185 -=== Opening an EBRAINS 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"
186 186  
187 -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.
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
188 188  
189 -=== Non-linear registration ===
174 + - allow the image service to access your bucket
190 190  
191 -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.
192 -1. Select the waln file corresponding to your result from the WebAlign image registration.
193 -1. Wait for the images to load: this may take some time.
176 +[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]
194 194  
195 -[[~[~[image:image1.png~|~|alt="_images/image1.png"~]~]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
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 -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.
180 +[[image:create collab.png||height="427" width="900"]]
198 198  
199 - 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.
182 +- Customize your ingestion:
200 200  
201 - 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.
184 + - give a name to your ingestion in the "description of ingestion" field.
202 202  
203 - 6. Press Delete or Backspace to remove a marker under the mouse cursor.
186 +**3. For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
204 204  
205 - 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.
188 +**4. Click //"preview"// in order to preview your task**
206 206  
207 - 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”.
190 +**5. Click //"create task"//  to launch your ingestion**
208 208  
192 +**6. Checking results in the Main UI page**
209 209  
210 -
194 +Press "Task" in the higher right corner of the window.
211 211  
212 -== **How to use LocaliZoom** ==
196 +When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
213 213  
214 -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.
198 +Otherwise, you will be redirected to the tasks list where the created task is selected.
215 215  
216 -Online Manual: [[https:~~/~~/localizoom.readthedocs.io/en/latest/>>https://localizoom.readthedocs.io/en/latest/]]
200 +//Note! //A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"
217 217  
202 +Refresh your browser in order to check the status of your task.
203 +
204 +When "successful", your chunks have been created.
205 +
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 +
218 218  The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
219 219  
220 220  === Opening a sample dataset ===
221 221  
222 - A demo dataset is loaded using the file: demo_mouse_data_lz
216 +Demo dataset is loaded using the file: **demo_mouse_data_start**
223 223  
224 -=== Opening a private or EBRAINS dataset ===
218 +You can see the result of a finished anchoring by choosing the file: **demo_mouse_data**
225 225  
226 -LocaliZoom will open all WebAlign (.waln) or WebWarp (.wwrp) files.
220 +=== Opening a private dataset ===
227 227  
228 -=== 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.
229 229  
230 -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
231 231  
232 -Press "delete" in order to remove an annotation.
226 +2. WebAlign will search for DZI files and list those found.
233 233  
234 -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.
235 235  
236 -=== Export of coordinate points ===
230 +4. Choose the target 3D reference atlas (WHSv3 for Rat and CCFv3_2017 for Mouse).
237 237  
238 -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.
239 239  
240 -The saved .lz file can also be visualised in the 3D viewer, MeshView.
234 +=== Registration instructions ===
241 241  
242 -== **How to use MeshView** ==
236 +**Short keys**
243 243  
244 -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).
245 245  
246 -Online manual: [[https:~~/~~/meshview-for-brain-atlases.readthedocs.io/en/latest>>https://meshview-for-brain-atlases.readthedocs.io/en/latest]]
246 +**Start the registration**
247 247  
248 -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.
249 249  
250 -=== Open point cloud files ===
250 +-If necessary, change the atlas from coronal view to sagittal or horizontal view (see Navigation panel below)
251 251  
252 -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.
253 253  
254 -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.
255 255  
256 -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.
257 257  
258 -=== Export images ===
258 +-If there is no marker, or the marker is a cross, mouse drag slides the cut in its plane (translation).
259 259  
260 -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):
261 261  
262 -[[image:image19.png]]
262 + -Left/Right arrow keys: marker becomes a vertical line, and mouse drag horizontally resizes the cut
263 263  
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)
264 264  
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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