ImageJ Macros

This workflow detects spots in a 2D image by filtering the image by Laplacian of Gaussian (user defined radius) and detecting regional intensity minima (user defined noise tolerance).

The macro will segment nuclei and separate clustered nuclei in a 3D image using a distance transform watershed. As a result an index-mask image is written for each input image.

The macro will segment nuclei and separate clustered nuclei using a binary watershed. As a result an index-mask image is written for each input image.

CLIJ2 is a GPU-accelerated image processing library for ImageJ/Fiji, Icy, Matlab and Java. It comes with hundreds of operations for filtering, binarizing, labeling, measuring in images, projections, transformations and mathematical operations for images. While most of these are classical image processing operations, CLIJ2 also allows performing operations on matrices potentially representing neighborhood relationships between cells and pixels.

CLIJ2 was developed to process images from fluorescence microscopy data of developing cells, tissues, organoids and organisms.

InspectJ is a free ImageJ/FIJI tool to inspect digital image integrity.

InspectJ_v2 is a newer version for advanced users. It applies additional features like histogram equalization and gamma correction for improved image inspections.