A093 - MorphoNet : How to segment a 3D dataset in just a few clicks?

Emmanuel Faure (???)
Tao Laurent (tao.laurent@lirmm.fr)

MorphoNet is an interactive morphodynamic web browser designed to help scientists, teachers and students share, analyze and visualize the large 3D morphological datasets that can be generated by modern imaging technology, ranging from live light sheet microscopy of cells and embryos to X Ray tomography of fossils. MorphoNet is created so that biologists can interact, without programming skills, with the 3D + time datasets. We have developed a web-based system so that they do not have to install any sophisticated software on their computers, and to allow data sharing. In a similar way as genomic browsers display genetic features and epigenetic or gene expression data as traces onto the primary genome sequence, quantitative and qualitative information can be imported and projected onto individual or grouped segmented objects in MorphoNet. These "morphological augmentations'' can be saved and shared with other users (and used in publications), respecting the FAIR philosophy. Moreover, MorphoNet offers more flexibility than genome browsers. While the DNA base pair is the universal unit of information in genome browsers, the relevant units of information can vary within imaging datasets, from complex organs down to molecular complexes. The choice of the unit of information is therefore left to the user. Objects can also be hidden, made translucent or hierarchically grouped: spatially (e.g., by tissue), temporally (e.g., by cell lineages), by imaging channels (e.g., nuclei and plasma membranes), and identified with specific color labels. We propose in this workshop to show you how to load raw intensity images in order to perform an interactive 3D segmentation. With the help of various plugins dedicated for 3D images segmentation, we will use various examples to illustrate the process of interactive 3d segmentation.