library

BIRL stands for "Benchmark on Image Registration methods with Landmark validation". BIRL is a cross-platform framework for comparison of image registration methods with landmark validation (registration precision is measured by user landmarks). The project contains a set of sample images with related landmark annotations and experimental evaluation of state-of-the-art image registration methods.

Some key features of the framework:

• automatic execution of image registration of a sequence of image pairs
• integrated evaluation of registration performances using Target Registration Error (TRE)
• integrated visualization of performed registration
• running several image registration experiment in parallel
• resuming unfinished sequence of registration benchmark
• handling around dataset and creating own experiments
• rerun evaluation and visualisation for finished experiments

Collection of several basic standard image segmentation methods focusing on medical imaging. In particular, the key block/applications are (un)supervised image segmentation using superpixels, object centre detection and region growing with a shape prior. Besides the open-source code, there is also a few sample images.

A set of ImageJ Built-in Macro Functions used to perform operations on the ImageJ platform.

The goal of mamut2r is to imports data coming from .xml files generated with the Fiji MaMuT plugin for lineage and tracking of biological objects. {mamut2r} also allows to create lineage plots.

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.