These macro scripts, developed for use with Fiji (ImageJ), enables batch processing of single-channel images acquired using the TruLive3D Imager Light-Sheet Fluorescence Microscopy (LSFM) system (Luxendo GmbH, Heidelberg, Germany).
N1_Image_opener.ijm.ijm.ijm automatically imports the datasets without much manual intervention;
N2_Adjust_BR.ijm.ijm.ijm adjusts the brightness of all opened images;
N3_Split_stack.ijm.ijm.ijm aplits the Z-stacks into individual images (.tif) and saves them in a single folder;
N4_Viability_calculations_LSFM_CAM.ijm was forked and modified from here : sophie-mountcastle/Biofilm-Viability-Checker
It analyzes Calcein AM-stained biofilms by quantifying the number of CAM-positive pixels, providing a measure of viable cell area. In addition, the script generates and saves overlay images that visually highlight the detected bacterial regions.