CU-MacroLibrary

ImageJ2 macro library with variables and functions

Software requirements

CU-MacroLibrary requires a recent version of the Fiji image processing package:

• ImageJ2 executable (>= 1.53e)
• Bio-Formats plugin (>= 6.4.0)

Software installation

To install the CU-MacroLibrary with your copy of Fiji, simply copy the Library.txt to Fiji.app\macros\ and its content will be available to any executed or installed macro. In addition, ImageJ2's macro editor will autocomplete function names from the library.

Available macro functions (selection)

• endsWithEither: simple test if a string ends with suffixes from a list.
• getFilesInFolder: returns a list of files matching a suffix patterns.
• getMedian: calculates the median value within given threshold values.
• getMedianValue: calculates the median value for a given array.
• getRegionOverlap: calculates the relative overlap between two ROI Manager regions.
• getRoisFromMasks: populates the ROI Manager with regions identified from a segmentation mask.
• normalizePixelValues: normalizes the pixel intensities of an image by its median value.
• readImage: reads image files with Bio-Format and labels the slices with the channel names.
• rescalePixelValues: rescales pixel intensities to a custom range, including NaN values.
• setMasksFromRois: creates a segmentation mask from available ROI Manager regions.
• substractRegions: implements the missing Substract function for the ROI Manager.
• toggleBatchMode: improves performance for image processing, selections, and ROI Manager updates.
• waitForWindow: halts the macro progression until a window with a specific title is available.

Copyright notices

The ImageJ2 image is part of the GitHub Pages for ImageJ.