by Keyword: Image analysis

Martinez A, Hériché JK, Calvo M, Tischer C, Otxoa-de-Amezaga A, Pedragosa J, Bosch A, Planas AM, Petegnief V, (2023). Characterization of microglia behaviour in healthy and pathological conditions with image analysis tools Open Biology 13, 220200

Microglia are very sensitive to changes in the environment and respond through morphological, functional and metabolic adaptations. To depict the modifications microglia undergo under healthy and pathological conditions, we developed free access image analysis scripts to quantify microglia morphologies and phagocytosis. Neuron-glia cultures, in which microglia express the reporter tdTomato, were exposed to excitotoxicity or excitotoxicity + inflammation and analysed 8 h later. Neuronal death was assessed by SYTOX staining of nucleus debris and phagocytosis was measured through the engulfment of SYTOX+ particles in microglia. We identified seven morphologies: round, hypertrophic, fried egg, bipolar and three 'inflamed' morphologies. We generated a classifier able to separate them and assign one of the seven classes to each microglia in sample images. In control cultures, round and hypertrophic morphologies were predominant. Excitotoxicity had a limited effect on the composition of the populations. By contrast, excitotoxicity + inflammation promoted an enrichment in inflamed morphologies and increased the percentage of phagocytosing microglia. Our data suggest that inflammation is critical to promote phenotypical changes in microglia. We also validated our tools for the segmentation of microglia in brain slices and performed morphometry with the obtained mask. Our method is versatile and useful to correlate microglia sub-populations and behaviour with environmental changes.

JTD Keywords: classification, identification, image analysis, injury, morphometry, neuroinflammation, neurotoxicity, phagocytosis, Classification, Image analysis, Microglia, Morphometry, Neuroinflammation, Nitric-oxide, Phagocytosis

Aviles, A. I., Sobrevilla, P., Casals, A., (2014). An approach for physiological motion compensation in robotic-assisted cardiac surgery Experimental & Clinical Cardiology , 20, (11), 6713-6724

The lack of physiological motion compensation is a major problem in robotic-assisted cardiac surgery. Since the heart is beating while the surgeon carried out the procedure, dexterity of the surgeon’s and precision are compromised. Due to the operative space and the visibility of the surgical field are reduced, the most practical solution is the use of computer vision techniques. The lack of efficiency and robustness of the existing proposals make physiological motion compensation to be considered an open problem. In this work a novel solution to solve this problem based on the minimization of an energy functional is presented. It is described in the three-dimensional space using the l1−regularized optimization class in which cubic b-splines are used to represent the changes produced on the heart surface. Moreover, the logarithmic barrier function is applied to create an approximation of the total energy in order to avoid its non-differentiability. According to the results, this proposal is able to deal with complex deformations, requires a short computational time and gives a small error.

JTD Keywords: Beating heart surgery, Image analysis, Motion compensation

Melchels, Ferry P. W., Tonnarelli, Beatrice, Olivares, Andy L., Martin, Ivan, Lacroix, Damien, Feijen, Jan, Wendt, David J., Grijpma, Dirk W., (2011). The influence of the scaffold design on the distribution of adhering cells after perfusion cell seeding Biomaterials 32, (11), 2878-2884

In natural tissues, the extracellular matrix composition, cell density and physiological properties are often non-homogeneous. Here we describe a model system, in which the distribution of cells throughout tissue engineering scaffolds after perfusion seeding can be influenced by the pore architecture of the scaffold. Two scaffold types, both with gyroid pore architectures, were designed and built by stereolithography: one with isotropic pore size (412 ± 13 [mu]m) and porosity (62 ± 1%), and another with a gradient in pore size (250-500 [mu]m) and porosity (35%-85%). Computational fluid flow modelling showed a uniform distribution of flow velocities and wall shear rates (15-24 s-1) for the isotropic architecture, and a gradient in the distribution of flow velocities and wall shear rates (12-38 s-1) for the other architecture. The distribution of cells throughout perfusion-seeded scaffolds was visualised by confocal microscopy. The highest densities of cells correlated with regions of the scaffolds where the pores were larger, and the fluid velocities and wall shear rates were the highest. Under the applied perfusion conditions, cell deposition is mainly determined by local wall shear stress, which, in turn, is strongly influenced by the architecture of the pore network of the scaffold.

JTD Keywords: Scaffolds, Microstructure, Cell adhesion, Confocal microscopy, Image analysis, Computational fluid dynamics