Useful scripts for saving multichannel fluorescence images for use in figures and saving relevant metadata
- This script was made to save and export images from Fiji for use in scientific figures after adjusting an image's settings.
- After opening the image and adjusting to your liking (including or excluding LUTs), run the macro
- To run, you can drag and drop into Fiji or Install it using Plugins... > Macros... > Install
- The macro will first prompt you to select a folder to save the output in. Within this folder, it will generate 1 folder per image to contain all associated files.
- The macro will then prompt you to select LUTs for each channel (if nothing is entered, will default to what is currently selected), enter metadata like the region you're looking at and relevant notes, and will allow you to optionally add a scale bar or inset.
- Scale bar length is determined automatically based on the image's metadata and the length is available in the log file generated by the script
- Insets allow the user to draw a rectangle in the image and will 1) Duplicate this selection and save it as its own image and 2) create an overlay on the original image showing where the inset was taken from.
- Multiple insets can be selected from the same image.
- Outputs: log file with information about B&C settings, notes, channel names, tiff files for each image channel (grayscale) and merged image (with LUTs) and inset with B&C settings preserved:
