Free and open source


Image segmentation and object detection performance measures

The goal of this package is to provide easy-to-use tools for evaluation of the performance of segmentation methods in biomedical image analysis and beyond, and to fasciliate the comparison of different methods by providing standardized implementations. This package currently only supports 2-D image data.

has function

SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.


MATLAB app to characterize nanoparticles imaged with super-resolution microscopy. nanoFeatures will read text and csv files from the NIKON and ONI microscopes and from the ThunderSTORM Fiji plugin, then cluster the localizations and filter by size and sphericity and finally output nanoparticle features like size, aspect ratio, and number of localizations per cluster (total and for each channel).

GUI first tab to browse and input files, select input type and check extra filters if needed.

These are commands that create or process binary (black and white) images. Typical morphological operations/functions can be found here.

need a thumbnail

ELEPHANT is a platform for 3D cell tracking, based on incremental and interactive deep learning.
It implements a client-server architecture. The server is built as a web application that serves deep learning-based algorithms. The client application is implemented by extending Mastodon, providing a user interface for annotation, proofreading and visualization.