Section: New Results

Grouped Local Automated Cell Extractor (GLACE )

Participants : Gaël Michelin, Grégoire Malandain.

This work is made in collaboration with Julien Laussu, Patrick Lemaire (CRBM, CNRS, Montpellier 1 & 2 university), Emmanuel Faure (IRIT, CNRS, Toulouse) and Christophe Godin (Inria Virtual Plants team, Montpellier).

In developmental biology, the embryogenesis study relies in particular on image-based studies. Today, fluorescent confocal microscopy is a means for in vivo imaging of developing organisms at cell level with a high spatio-temporal resolution. To handle such 3D+$t$ image sequences, adapted computer-assisted methods are highly desirable in order to extract essential information from these data.

More specifically, for developing ascidian embryos, an existing framework called ASTEC   [19] is used by biologists in order to extract the cell segmentation and lineage from some 3D+$t$ sequences. However, remaining issues about segmentation accuracy motivated us to propose a new framework as an alternative to ASTEC for cell segmentation and tracking. The originality of the proposed Grouped Local Automated Cell Extractor (GLACE ) framework is to segment the $i$–th image of a sequence by applying locally the original 3D cell segmentation framework of  [21] for all the regions of interest defined by the segmented cells of the $i-1$–th image of the sequence. The union of all the local reconstructions provides the segmentation of the $i$–th image of the sequence (figure 11). The GLACE framework does not replace the ASTEC framework, however they provide complementary results for embryo image sequence reconstructions.

Figure 11. Pipeline for GLACE .