***Note/Disclaimer: These macros are relatively simple and straightforward to modify for your own uses. I wrote them to solve simple tasks that I repeatedly must do for my image analysis pipeline. They are mostly designed to save you the headache of performing simple, menial tasks over and over. Please feel free to modify them for your specific individual purposes. I do not claim any responsibility for any data or images that comes from using these scripts. If you plan to publish data that you have modified using these macros/plugins, it is YOUR responsibility to make sure you understand exactly what is being done to your images and that no unforeseen artifacts arise as a result. Please be sure to read the comments in the scripts before using them.

FIJI/ImageJ Macros

Type Conversion

hyperstack_to_8bit.ijm Converts hyperstacks in a directory of the user's choosing to 8bit hyperstacks.

Stack Rearrangement

delete_ch_x_of_3_batch.ijm Deletes channel 1, 2 or 3 from a directory of 3-channel hyperstacks.

split_stack_and_save_batch.ijm Splits a directory of multi-channel single frame images into the separate channels and saves the channels as new images.

stack_to_merge_2_ch_batch.ijm Makes merge images from 2-channel image series and saves as new images. Can easily be modified for more channels.

stack_to_montage_2_color.ijm Saves a ch1/ch2/merge montage of a single 2 color image with an option to add a scale bar.


copy_results_field.ijm Copies a field (column) from the results table in FIJI/ImageJ to the system clipboard. (Very useful if you need to copy the results from measurements in FIJI to a spreadsheet, for example.)

More macros coming soon...