Proceedings of the National Academy of Sciences, 2020
Significance Although ACh is best known for its role in neurotransmission, it also plays a role i... more Significance Although ACh is best known for its role in neurotransmission, it also plays a role in cell migration. ACh promotes various cell migrations in vitro, but little is known how it affects cell migration inside an organism where multiple environmental cues are involved. We investigated the migration of an epithelial cell in C. elegans , the gonad leader cell, which expresses a muscarinic acetylcholine receptor. This leader cell migrates closely along the animal’s nerve cords and uses ACh secreted from cholinergic neurons. The muscarinic receptor helps the leader cell stay on its migratory path, but its overactivation causes a reversal in cell orientation. The leader cell may use the muscarinic receptor to adjust its orientation to stay on its migratory path.
2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), 2019
We present an algorithm to compute the geometric median of shapes which is based on the extension... more We present an algorithm to compute the geometric median of shapes which is based on the extension of median to high dimensions. The median finding problem is formulated as an optimization over distances and it is solved directly using the watershed method as an optimizer. We show that the geometric median shape faithfully represents the true central tendency of the data, contaminated or not. It is superior to the mean shape which can be negatively affected by the presence of outliers. Our approach can be applied to manifold and non manifold shapes, with single or multiple connected components. The application of distance transform and watershed algorithm, two well established constructs of image processing, lead to an algorithm that can be quickly implemented to generate fast solutions with linear storage requirement. We demonstrate our methods in synthetic and natural shapes and compare median and mean results under increasing outlier contamination.
hybridization based on the mechanism of the hybridization chain reaction (HCR) has addressed mult... more hybridization based on the mechanism of the hybridization chain reaction (HCR) has addressed multi-decade challenges that impeded imaging of mRNA expression in diverse organisms, offering a unique combination of multiplexing, quantitation, sensitivity, resolution and versatility. Here, with third-generation HCR, we augment these capabilities using probes and amplifiers that combine to provide automatic background suppression throughout the protocol, ensuring that reagents will not generate amplified background even if they bind non-specifically within the sample. Automatic background suppression dramatically enhances performance and robustness, combining the benefits of a higher signal-to-background ratio with the convenience of using unoptimized probe sets for new targets and organisms. HCR v3.0 enables three multiplexed quantitative analysis modes: (1) qHCR imaging - analog mRNA relative quantitation with subcellular resolution in the anatomical context of whole-mount vertebrate e...
2012 IEEE 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, 2012
ABSTRACT We survey useful ingredients for a new class of mathematical process-modeling languages ... more ABSTRACT We survey useful ingredients for a new class of mathematical process-modeling languages aimed at spatial and developmental biology. Existing modeling languages for computational systems biology do not fully address the problems of spatial modeling that arise in morphodynamics (the local dynamics of form) and its applications to biological development. We seek to extend the operator algebra semantics approach from our previous “Dynamical Grammars” modeling language, whose most spatial object type is the labelled graph, to encompass more flexible topological objects. Taking clues from current developments in 3D meshing and from topological modeling for biology, illustrated by a plant tissue example, we seek language support for the approximation of low-dimensional CW complexes (which are nontrivial topological spaces, with cardinality of the continuum) and dynamic fields thereon, by finite labelled abstract complexes. Some of the proposed types would be computationally demanding, without further restriction. Restrictions and control of these approximations can be specified by use of “metricated” types. Minimally, such approximations should permit the accurate simulation of spatial diffusion processes.
We present an algorithm to compute the geometric median of shapes which is based on the extension... more We present an algorithm to compute the geometric median of shapes which is based on the extension of median to high dimensions. The median finding problem is formulated as an optimization over distances and it is solved directly using the watershed method as an optimizer. We show that computing the geometric median of shapes is robust in the presence of outliers and it is superior to the mean shape which can easily be affected by the presence of outliers. The geometric median shape thus faithfully represents the true central tendency of the data, contaminated or not. Our approach can be applied to manifold and non manifold shapes, with connected or disconnected shapes. The application of distance transforms and watershed algorithm, two well established constructs of image processing, lead to an algorithm that can be quickly implemented to generate fast solutions with linear storage requirements. We demonstrate our methods in synthetic and natural shapes and compare median and mean r...
1 ABSTRACT The numerical solution of problems in science and engineering via the finite element m... more 1 ABSTRACT The numerical solution of problems in science and engineering via the finite element method requires, as a first step, the discretization of a domain into a set of simply shaped elements. Determining the size of these elements along the domain, including the ...
We present an efficient algorithm for nonlocal image filtering with applications in electron cryo... more We present an efficient algorithm for nonlocal image filtering with applications in electron cryomicroscopy. Our denoising algorithm is a rewriting of the recently proposed nonlocal mean filter. It builds on the separable property of neighborhood filtering to offer a fast ...
Proceedings of the National Academy of Sciences, 2020
Significance Although ACh is best known for its role in neurotransmission, it also plays a role i... more Significance Although ACh is best known for its role in neurotransmission, it also plays a role in cell migration. ACh promotes various cell migrations in vitro, but little is known how it affects cell migration inside an organism where multiple environmental cues are involved. We investigated the migration of an epithelial cell in C. elegans , the gonad leader cell, which expresses a muscarinic acetylcholine receptor. This leader cell migrates closely along the animal’s nerve cords and uses ACh secreted from cholinergic neurons. The muscarinic receptor helps the leader cell stay on its migratory path, but its overactivation causes a reversal in cell orientation. The leader cell may use the muscarinic receptor to adjust its orientation to stay on its migratory path.
2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), 2019
We present an algorithm to compute the geometric median of shapes which is based on the extension... more We present an algorithm to compute the geometric median of shapes which is based on the extension of median to high dimensions. The median finding problem is formulated as an optimization over distances and it is solved directly using the watershed method as an optimizer. We show that the geometric median shape faithfully represents the true central tendency of the data, contaminated or not. It is superior to the mean shape which can be negatively affected by the presence of outliers. Our approach can be applied to manifold and non manifold shapes, with single or multiple connected components. The application of distance transform and watershed algorithm, two well established constructs of image processing, lead to an algorithm that can be quickly implemented to generate fast solutions with linear storage requirement. We demonstrate our methods in synthetic and natural shapes and compare median and mean results under increasing outlier contamination.
hybridization based on the mechanism of the hybridization chain reaction (HCR) has addressed mult... more hybridization based on the mechanism of the hybridization chain reaction (HCR) has addressed multi-decade challenges that impeded imaging of mRNA expression in diverse organisms, offering a unique combination of multiplexing, quantitation, sensitivity, resolution and versatility. Here, with third-generation HCR, we augment these capabilities using probes and amplifiers that combine to provide automatic background suppression throughout the protocol, ensuring that reagents will not generate amplified background even if they bind non-specifically within the sample. Automatic background suppression dramatically enhances performance and robustness, combining the benefits of a higher signal-to-background ratio with the convenience of using unoptimized probe sets for new targets and organisms. HCR v3.0 enables three multiplexed quantitative analysis modes: (1) qHCR imaging - analog mRNA relative quantitation with subcellular resolution in the anatomical context of whole-mount vertebrate e...
2012 IEEE 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, 2012
ABSTRACT We survey useful ingredients for a new class of mathematical process-modeling languages ... more ABSTRACT We survey useful ingredients for a new class of mathematical process-modeling languages aimed at spatial and developmental biology. Existing modeling languages for computational systems biology do not fully address the problems of spatial modeling that arise in morphodynamics (the local dynamics of form) and its applications to biological development. We seek to extend the operator algebra semantics approach from our previous “Dynamical Grammars” modeling language, whose most spatial object type is the labelled graph, to encompass more flexible topological objects. Taking clues from current developments in 3D meshing and from topological modeling for biology, illustrated by a plant tissue example, we seek language support for the approximation of low-dimensional CW complexes (which are nontrivial topological spaces, with cardinality of the continuum) and dynamic fields thereon, by finite labelled abstract complexes. Some of the proposed types would be computationally demanding, without further restriction. Restrictions and control of these approximations can be specified by use of “metricated” types. Minimally, such approximations should permit the accurate simulation of spatial diffusion processes.
We present an algorithm to compute the geometric median of shapes which is based on the extension... more We present an algorithm to compute the geometric median of shapes which is based on the extension of median to high dimensions. The median finding problem is formulated as an optimization over distances and it is solved directly using the watershed method as an optimizer. We show that computing the geometric median of shapes is robust in the presence of outliers and it is superior to the mean shape which can easily be affected by the presence of outliers. The geometric median shape thus faithfully represents the true central tendency of the data, contaminated or not. Our approach can be applied to manifold and non manifold shapes, with connected or disconnected shapes. The application of distance transforms and watershed algorithm, two well established constructs of image processing, lead to an algorithm that can be quickly implemented to generate fast solutions with linear storage requirements. We demonstrate our methods in synthetic and natural shapes and compare median and mean r...
1 ABSTRACT The numerical solution of problems in science and engineering via the finite element m... more 1 ABSTRACT The numerical solution of problems in science and engineering via the finite element method requires, as a first step, the discretization of a domain into a set of simply shaped elements. Determining the size of these elements along the domain, including the ...
We present an efficient algorithm for nonlocal image filtering with applications in electron cryo... more We present an efficient algorithm for nonlocal image filtering with applications in electron cryomicroscopy. Our denoising algorithm is a rewriting of the recently proposed nonlocal mean filter. It builds on the separable property of neighborhood filtering to offer a fast ...
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Papers by Alexandre Cunha