DSpace Collection:
https://hdl.handle.net/10171/52018
2024-03-28T12:08:30ZNMF-RI: blind spectral unmixing of highly mixed multispectral flow and image cytometry data
https://hdl.handle.net/10171/68835
Title: NMF-RI: blind spectral unmixing of highly mixed multispectral flow and image cytometry data
Abstract: Motivation
Recent advances in multiplex immunostaining and multispectral cytometry have opened the door to simultaneously visualizing an unprecedented number of biomarkers both in liquid and solid samples. Properly unmixing fluorescent emissions is a challenging task, which normally requires the characterization of the individual fluorochromes from control samples. As the number of fluorochromes increases, the cost in time and use of reagents becomes prohibitively high. Here, we present a fully unsupervised blind spectral unmixing method for the separation of fluorescent emissions in highly mixed spectral data, without the need for control samples. To this end, we extend an existing method based on non-negative Matrix Factorization, and introduce several critical improvements: initialization based on the theoretical spectra, automated selection of ‘sparse’ data and use of a re-initialized multilayer optimizer.
Results
Our algorithm is exhaustively tested using synthetic data to study its robustness against different levels of colocalization, signal to noise ratio, spectral resolution and the effect of errors in the initialization of the algorithm. Then, we compare the performance of our method to that of traditional spectral unmixing algorithms using novel multispectral flow and image cytometry systems. In all cases, we show that our blind unmixing algorithm performs robust unmixing of highly spatially and spectrally mixed data with an unprecedently low computational cost. In summary, we present the first use of a blind unmixing method in multispectral flow and image cytometry, opening the door to the widespread use of our method to efficiently pre-process multiplex immunostaining samples without the need of experimental controls.2020-01-01T00:00:00ZSystematic method for morphological reconstruction of the semicircular canals using a fully automatic skeletonization process
https://hdl.handle.net/10171/68832
Title: Systematic method for morphological reconstruction of the semicircular canals using a fully automatic skeletonization process2019-01-01T00:00:00ZInstabilities triggered in different conducting fluid geometries due to slowly time-dependent magnetic fields
https://hdl.handle.net/10171/68830
Title: Instabilities triggered in different conducting fluid geometries due to slowly time-dependent magnetic fields
Abstract: The main objective of this work is the study and analysis of non-linearities forced through oscillating magnetic fields in a conducting fluid where the instabilities are triggered due to magnetohydrodynamic forces. Different geometries have been studied and different surface patterns that break the symmetries have been observed. First, an InGaSn drop of fluid where the system breaks the azimuthal and radial symmetries depending on the volume is observed. Second, we extend the study to an InGaSn annular configuration where the presence of patterns opens the door to discuss the possibility to extend these results to other configurations as biological systems, where the conducting fluid is an electrolyte. This configuration has an added interest, as it has been proposed that the vertigoes triggered on patients in an MRI test could be generated by the interaction of the magnetic field with the electrolyte present in the inner ear.2018-01-01T00:00:00ZExperimental dynamics in magnetic field-driven flows compared to thermoconvective convection
https://hdl.handle.net/10171/68825
Title: Experimental dynamics in magnetic field-driven flows compared to thermoconvective convection
Abstract: We compare the dynamics obtained in two intermediate aspect ratio (diameter over height) experiments. These systems have rotational symmetry and consist of fluid layers that are destabilized using two different methods. The first one is a classical Bénard–Marangoni experiment, where the destabilizing forces, buoyancy and surface tension, are created by temperature gradients. The second system consists of a large drop of liquid metal destabilized using oscillating magnetic fields. In this configuration, the instability is generated by a radial Lorentz force acting on the conducting fluid. Although there are many important differences between the two configurations, the dynamics are quite similar: the patterns break the rotational symmetry, and different azimuthal and radial wavenumbers appear depending on the experimental control parameters. These patterns in most cases are stationary, but for some parameters they exhibit different dynamical behaviours: rotations, transitions between different solutions or cyclic connections between different patterns.2015-01-01T00:00:00Z