Bioimaging of animal embryogenesis:
mathematical methods and computational algorithms
Rizzi, Barbara <1973>
Subject
ING-INF/06 Bioingegneria elettronica e informatica
Description
Some fundamental biological processes such as embryonic development have been preserved
during evolution and are common to species belonging to different phylogenetic
positions, but are nowadays largely unknown. The understanding of cell morphodynamics
leading to the formation of organized spatial distribution of cells such as tissues
and organs can be achieved through the reconstruction of cells shape and position during
the development of a live animal embryo. We design in this work a chain of image
processing methods to automatically segment and track cells nuclei and membranes
during the development of a zebrafish embryo, which has been largely validates as
model organism to understand vertebrate development, gene function and healingrepair
mechanisms in vertebrates. The embryo is previously labeled through the ubiquitous
expression of fluorescent proteins addressed to cells nuclei and membranes, and
temporal sequences of volumetric images are acquired with laser scanning microscopy.
Cells position is detected by processing nuclei images either through the generalized
form of the Hough transform or identifying nuclei position with local maxima after a
smoothing preprocessing step. Membranes and nuclei shapes are reconstructed by using
PDEs based variational techniques such as the Subjective Surfaces and the Chan Vese
method. Cells tracking is performed by combining informations previously detected
on cells shape and position with biological regularization constraints. Our results are
manually validated and reconstruct the formation of zebrafish brain at 7-8 somite stage
with all the cells tracked starting from late sphere stage with less than 2% error for
at least 6 hours. Our reconstruction opens the way to a systematic investigation of
cellular behaviors, of clonal origin and clonal complexity of brain organs, as well as the
contribution of cell proliferation modes and cell movements to the formation of local
patterns and morphogenetic fields.
Rizzi, Barbara (2009) Bioimaging of animal embryogenesis: mathematical methods and computational algorithms, [Dissertation thesis], Alma Mater Studiorum Università di Bologna. Dottorato di ricerca in Bioingegneria , 21 Ciclo.