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