Changes for page 1. Setting up the working environment
Last modified by puchades on 2025/02/13 10:43
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... ... @@ -68,106 +68,3 @@ 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)