Useful single-run scripts for Fiji ImageJ's batch analysis of cell plates.
Image files MUST follow this Gen5 naming convention from the C10 for script-compatibility:
<READ_STEP_SEQUENCE><CHANNEL_INDEX><IMAGE_IN_WELL_INDEX>_<READ_INDEX>.tif
Example: A1_01_1_1_DAPI_001.tif
Creates customized montage images from a folder of source TIFs. UI-enabled. Drag-and-drop into ImageJ and click run.
Allows files from a folder and subdirectory to be batch-renamed. On first usage, enter the folder of interest and it will generate a manifest of files inside the folder in an Excel workbook. Enter the new filename for each file in the second column, exit the workbook and follow the prompts. Run in terminal with a command line interface.
Creates montaged images from a folder of source TIFs based on a specific well configuration for 384-well plates used for drug screens. UI-enabled. Drag-and-drop into ImageJ and click run.