A small collection of useful macro for Fiji (ImageJ).
SLD_image_exporter.ijm: Batch exports and converts Slidebook (.sld) files to .tif. Requires the Slidebook update site.
Count_ROI_per_Slice.ijm: Counts ROIs per frame in an image stack with one channel and multiple slices. Outputs ROI counts and differences to the console.
Measure_Intensity_All_Slices.ijm: Measures intensity for all slices in a stack. Iterates through each slice, setting and measuring the current slice.
Run_Analyse_particle_on_all_ROI.ijm: Runs the Analyze Particles function on all ROIs in the ROI Manager. Iterates through each ROI, selecting and analyzing particles.
Batch_processing.ijm: Batch processing macro empty backbone. Just add your own code to process folders.
bitDepth_checker.ijm: Prints the bit-depth of each image in a folder.
Random_point_generation_ROI.ijm: An ImageJ macro that randomly generates points inside a binary mask. The script generates a specified number of random points, overlays them onto the image, and counts how many of them fall inside the region of interest (ROI) where the pixel value is 255.
Intensity_measurement_using_mask.ijm An ImageJ macro that opens the channel of interest and corresponding segmented mask image to measure the intensity based on the mask image.
ROIwithHoles_to_Label_images.ijm An ImageJ macro to convert ROIs with holes into label images. This macro was from Hanna and Sujan used for his doughnut masks.