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Set of tools to generate whole slide images from digital histological phantoms
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apgrgr/SyntheticWSI
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SyntheticWSI v201501300946 Requirements Java 8+ Quick start 1. Start the graphical interface (double-click or left-click and find "run as Java application" or "open with Java") 2. Click "Extract Example" (check that it generates a directory data/ with images and XML files) 3. Click "GenerateWSI"; the options are the paths of the model file and the renderer specification file (default values should point to files inside data/); click "Ok" 4. Wait... (depending on the hardware, it can be less than 30 min or more than 2h) 5. If all goes well, the previous step should: * generate a temporary directory with synthetic tiles and a corresponding ZIP archive: the directory can be deleted, the WSI is the ZIP file * generate a temporary file named renderers.jo: this contains the WSI description ("perfect ground truth") but is currently only used as an intermediate step in the WSI generation * display the generated WSI Possible issues * Not enough memory allocated to the program Solution: use the command line to start the application with more memory: java -Xmx16g -jar syntheticwsi.jar Graphical interface * README Show this file. * Extract Example Extract example files into the subdirectory data/ in the current directory * ModelMaker Start the tool to make "models" = 2D digital phantoms Ctrl+N: new texture/model Ctrl+O: open a texture/model file (XML) or load a background image (JPG, PNG, SVS) Ctrl+S: save the current texture/model Ctrl+C: copy current view to OS clipboard B: show/hide background image +/-: zoom in/out Ctrl+Left click: start new region Drag motion with left mouse button: extend current region Shift+Drag motion with left mouse button: reduce current region Right click: select texture (Mac OS X: use Cmd instead of Ctrl) * GenerateWSI Start the tool to generate a WSI (format = zipped JPG tiles) * ViewWSI Start the tool to visualize WSIs (drag and drop images from OS to open them) Command line interface * ModelMaker java -cp syntheticwsi.jar fr.unistra.wsi.synthetic.ModelMaker * GenerateWSI java -cp syntheticwsi.jar fr.unistra.wsi.synthetic.GenerateWSI [model <file path>] [renderer <file path>] [output <file path>] [tileWidth <integer>] [tileHeight <integer>] [show <0|1>] * ViewWSI java -cp syntheticwsi.jar imj2.zipslideviewer.ZipSlideViewer [file <file path>]
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Set of tools to generate whole slide images from digital histological phantoms