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68	68	Refresh your browser in order to check the status of your task.
69	69
70	70	When "successful", your chunks have been created.
71		-
72		-== What is WebAlign? ==
73		-
74		-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 is used for analysis in the online QUINT workflow.
75		-
76		-== **How to use WebAlign** ==
77		-
78		-The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
79		-
80		-=== Opening a sample dataset ===
81		-
82		-Demo dataset is loaded using the file:**demo_mouse_data_start**
83		-
84		-You can see the result of a finished anchoring by choosing the file: **demo_mouse_data**
85		-
86		-=== Opening a private dataset ===
87		-
88		-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.
89		-
90		-~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
91		-
92		-2. WebAlign will search for DZI files and list those found.
93		-
94		-3. Enter a name for the descriptor json file which will be created and will contain your anchoring information.
95		-
96		-4. Choose the target 3D reference atlas (WHSv3 for Rat and CCFv3_2017 for Mouse).
97		-
98		-5. Press //"create"//. The main window will now display WebAlign. This step can take some time.
99		-
100		-=== Registration instructions ===
101		-
102		-**Short keys**
103		-
104		-|=To do this|=Press|=Description
105		-|Place marker|Space bar|Markers are the anchor points of most transformations (stretch and rotate).
106		-|Remove marker|Esc|Removes a previously placed marker.
107		-|Horizontal stretch from marker |Left/Right arrow keys|Marker becomes a vertical line, and mouse drag horizontally resizes the cut.
108		-|Vertical stretch from marker |Up/Down arrow keys|Marker becomes a horizontal line, and mouse drag vertically resizes the cut
109		-|Rotate around marker|PgUp/PgDown|Marker becomes a cross with a surrounding arc, and mouse drag rotates the cut.
110		-|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).
111		-
112		-**Start the registration**
113		-
114		-The main window shows the selected image with the atlas overlay.
115		-
116		--If necessary, change the atlas from coronal view to sagittal or horizontal view (see Navigation panel below)
117		-
118		-~1. Move the atlas to the approximate position of your section using the yellow dots in the three small windows from the navigation panel.
119		-
120		-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.
121		-
122		-3. The main window supports mouse drag in multiple modes in order to stretch the atlas and find the correct position.
123		-
124		--If there is no marker, or the marker is a cross, mouse drag slides the cut in its plane (translation).
125		-
126		--Keyboard controls to modify mouse drag (they also place the marker if it's not placed already):
127		-
128		- -Left/Right arrow keys: marker becomes a vertical line, and mouse drag horizontally resizes the cut
129		-
130		- -Up/Down arrow keys: marker becomes a horizontal line, and mouse drag vertically resizes the cut
131		-
132		- -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.
133		-
134		-After each transformation step, marker resets to a cross (translation mode).
135		-
136		- //Note!// The panel can be resized towards the left (common border with Control Panel) and towards the bottom (common border with Filmstrip).
137		-
138		-4. Save the position by pressing //"Store". //The registration is copied to the remaining slides to help with scaling (visible also in the filmstrip)
139		-
140		-5. Go through all sections and refine position and cutting angles.
141		-
142		- //Note!// When jumping from one section to the other, wait a few seconds for the image to load
143		-
144		- //Note!// The "restore" button allows you to go back to the saved position if necessary
145		-
146		-6. Save your results in the descriptor file (json) by pressing "Save to bucket".
147		-
148		-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".//
149		-
150		-**Control panel:**
151		-
152		-|=Button|=Function
153		-|Store |Store the current alignment and propagate to unaligned sections (**Note** this does not save the series to your bucket)
154		-|Restore |Reset the current alignment to the last stored position
155		-|Clear |Reset the current alignment to the default position
156		-|Overlay Slider |Opacity of the atlas overlay, when fully opaque, it becomes an outline
157		-|Overlay color |The outline color
158		-|Filmstrip slider and color|The above settings, applied to the filmstrip
159		-|Save to bucket|Save the series to your bucket (and overwrite the existing file)
160		-|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)
161		-
162		-
163		-The right border of the control panel can be dragged horizontally, allowing to resize the panel and the main view
164		-
165		-**Filmstrip:**
166		-
167		-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
168		-
169		-**Navigation panel:**
170		-
171		-Shows the three standard planes centered around the midpoint of the current alignment visible in the main view.
172		-
173		-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.
174		-
175		-Drag the midpoint around to move the cut.
176		-
177		-Drag anywhere else to rotate the cut (inside the given standard plane, around the midpoint)