Join GitHub today
GitHub is home to over 50 million developers working together to host and review code, manage projects, and build software together.Sign up
Set of tools to generate whole slide images from digital histological phantoms
Fetching latest commit…
Cannot retrieve the latest commit at this time.
|Type||Name||Latest commit message||Commit time|
|Failed to load latest commit information.|
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>]