script to divide image into tiles

QuPath_workflow/GAT_divide_image_width.groovy

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+
+//If you'd like to study distribution of cells across the lenght of the tissue, you can use this script to divide image annotation into tiles
+//Create full image annotation
+//Perform detection using GAT script first
+// Run this script to divide the annotation into tiles of specified width (microns). You can specify tile width below
+
+
+
+//CHANGE WIDTH HERE (//in microns)
+//***************
+user_width = 100 
+//***************
+
+import qupath.lib.gui.dialogs.Dialogs
+
+println("Make sure you have a full image annotation using Objects -> Annotations ->Create full image annotation")
+
+def pathObjects = getSelectedObjects()
+if (pathObjects.isEmpty()) {
+Dialogs.showErrorMessage("GAT", "Please select a full image annotation!")
+return
+}
+//Create some sort of non-rectangular annotation first!
+
+def imageserver = getCurrentServer()
+def cal = imageserver.getPixelCalibration()
+pixel_size = cal.getPixelHeightMicrons()
+
+tissue = getAnnotationObjects()[0]
+
+roi = tissue.getROI()
+
+def plane = getCurrentViewer().getImagePlane()
+
+total_width = roi.getBoundsWidth()
+total_height = roi.getBoundsHeight()
+println(user_width)
+user_width = user_width/pixel_size
+println(user_width)
+no_tiles_init = total_width/user_width
+no_tiles= Math.ceil(no_tiles_init)
+last_tile_frac = 1-(no_tiles - no_tiles_init)
+println(no_tiles)
+println(no_tiles_init)
+println(last_tile_frac)
+x_top = 0
+y_top = 0
+for (i = 0; i < no_tiles; i++) {
+if(i==no_tiles-1 && last_tile_frac>0)
+{
+  user_width*=last_tile_frac
+}
+
+boundingROI = ROIs.createRectangleROI(
+            x_top, //top left corner
+            0, //top left corner
+            user_width, //width
+            total_height, //height
+            plane)
+x_top+=user_width;
+boundingAnnotation = PathObjects.createAnnotationObject(boundingROI)
+if(i<9)
+{
+  tile_name = 'Tile 00' 
+}
+else if (i<100)
+{
+  tile_name = 'Tile 0'
+}
+else tile_name = 'Tile ' 
+
+boundingAnnotation.setName(tile_name + (i+1))
+addObject(boundingAnnotation)
+}
+
+//resolve heirarchy to cells belong to each tile
+resolveHierarchy()