Bioimage informatics

Bioimage analysis

BIIGLE is a web-based software for image and video annotation that enables collaborative research on large datasets. It offers tools for manual and computer-assisted annotation, quality control and the collaboration on custom taxonomies to describe objects. BIIGLE is freely available and can be installed in cloud environments, a local network or on mobile platforms during research expeditions. The public instance on is free for non-commercial use.


TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaps can be used as a web service or locally in your computer, and allows users to share regions of interest and local statistics.


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.