def process_img(img_path): IJ.log('Processing {} ...'.format(img_path)) # open image imp = IJ.openImage(img_path) imp.show() w_big = imp.getWindow() w_big.setLocationAndSize(1050, 400, 500, 500) # read relative csv file rows (coordinates of centers) img_name, img_extension = os.path.splitext(img_path) marker_path = img_name + '.csv' if not os.path.exists(marker_path): root = os.path.dirname(marker_path) IJ.log('Creating corrected CSV files in {}...'.format(root)) mrk.markers_to_csv(root, y_inv_height=imp.height) markers = mrk.read_marker(marker_path, to_int=True) for cs in gen_cell_stacks(imp, markers, cube_roi_dim, scaleZ): # identify cell in original image imp.setSlice(cs.seed[2] + 1) point = PointRoi(cs.seed[0], cs.seed[1]) point.setSize(3) point.setColor(Color.RED) imp.setRoi(point) if discard_margin_cells: if not cs.onBorder: process_cell(cs) else: IJ.log('Skipped on border cell in seed ' + str(cs.seed)) else: process_cell(cs) c = raw_input( "Press enter to show the next cell or 'n' to go to the next image\n" ) cs.close() if c == 'n': IJ.log("Skipped remaining cells") break