Segmentation of cellular compartments

Segmentation adapted to each organelle

Every cellular compartment has a specific morphology, a fibrous structure cannot be thus segmented in the same way as a spot (like a kinetocore) or a round structure (like a nucleus). The detection of a compartment is a complex process which requires to parametrize finely segmentation tools to analyse correctly the fluorescent signal. Generally speaking, these groups of components are segmented in the same way (list is not exhaustive):

  • Fibers: strands of actine, microtubules, intermediate strands, extracellular matrix
  • Complex compartments: Golgi apparatus, endoplasmic reticulum, chromosomes during the mitosis,mitotic spindle, mitocondria, ribosome
  • Spots: endosomes, lysosomes, MOC, vacuoles, vesicles
  • Membrane: cytoplasmic membrane, nuclear membrane

Examples of segmentations adapted to centrosome, Golgi and nuclei

The segmentation of compartments allows to analyze their morphology (size, shape, intensity, position in the cell) and their position compared with other compartments.

compartiments cellulaires cellular compartments

The following figure illustrates the position of compartments in cells plated into micropatterns. Three cellular compartments are separately segmented: centrosomes, Golgi apparatus and nuclei. The figure A shows every compartment and its segmentation. The figure B shows the distributions of compartments in the space (centrosome in green, Golgi in red and nuclei in blue). The figure C represents vectors nuclei – centrosomes and their directions


Anisotropy of cell adhesive microenvironment governs cell internal organization and orientation of polarity.Théry M, Racine V, Piel M, Pépin A, Dimitrov A, Chen Y, Sibarita JB, Bornens M. Proc Natl Acad Sci U S A, 103(52):19771-6, 2006.

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