Papers by Edite Figueiras
An Optical Projection Tomography (OPT) system was developed and optimized to image 3D tissue engi... more An Optical Projection Tomography (OPT) system was developed and optimized to image 3D tissue engineered products based in hydrogels. We develop pre-reconstruction algorithms to get the best result from the reconstruction procedure, which include correction of the illumination and determination of sample center of rotation (CoR). Existing methods for CoR determination based on the detection of the maximum variance of reconstructed slices failed, so we develop a new CoR search method based in the detection of the variance sharpest local maximum. We show the capabilities of the system to give quantitative information of different types of hydrogels that may be useful in its characterization.
EMBEC & NBC 2017
Gellan gum is a hydrogel with potential for soft tissue engineering but a quick and thorough meth... more Gellan gum is a hydrogel with potential for soft tissue engineering but a quick and thorough method is needed for screening of different possible compositions for more extensive studies. Here optical projection tomography in bright field mode was used to image nearly transparent hydrogels to record their optical texture in 3D. The gained Haralick’s textural features were then analyzed with multiple discriminant analysis and combined with data from mechanical testing and neuronal cell culturing. We show the usefulness of optical texture analysis in screening of hydrogel compositions when aiming for tissue engineering applications.
This work presents an analysis of the performances for four different implementations used to com... more This work presents an analysis of the performances for four different implementations used to compute laser speckle contrast on images. Laser speckle contrast is a widely used imaging technique for biomedical applications. These implementations were tested using synthetic laser speckle patterns with different resolutions, speckle sizes, and contrasts. From the applied methods, three implementations are already known in the literature. A new alternative is proposed herein, which relies on two-dimensional convolutions, in order to improve the image processing time without compromising the contrast assessment. The proposed implementation achieves a processing time two orders of magnitude lower than the analytical evaluation. The goal of this technical manuscript is to help the developers and researchers in computing laser speckle contrast images.
Sensors, 2017
This short note presents an overview of some laser-baser methods used to extract hemodynamic para... more This short note presents an overview of some laser-baser methods used to extract hemodynamic parameters. The sensors and methods have been divided in two application fields, microcirculation and macrocirculation. For further readings about this subject please consult the cited references.
Tese de doutoramento em Fisica, especialidade de Fisica Tecnologica, apresentada a Faculdade de C... more Tese de doutoramento em Fisica, especialidade de Fisica Tecnologica, apresentada a Faculdade de Ciencias e Tecnologia da Universidade de Coimbra
We present a computational model describing the blurring of particles with respect to focal dista... more We present a computational model describing the blurring of particles with respect to focal distance in 3D optical imaging. The model can be used to improve reconstructions in optical projection tomography. OCIS codes: 100.6950, 170.6900.
Electrical impedance tomography (EIT) is a label free harmless imaging method capable of imaging ... more Electrical impedance tomography (EIT) is a label free harmless imaging method capable of imaging differences in electrical conductivity of a sample. In EIT, a low frequency current is injected into the sample, voltage differences on sample surface are measured, and from these measurements, interior conductivity distribution is reconstructed. To increase the accuracy of reconstruction, rotational EIT (rEIT) has been proposed where independent measurements are taken from multiple rotational positions around the sample. However, the benefit of conventional electrode configurations are limited to small number of rotational positions. We have presented an approach called Limited Angle Full Revolution rEIT (LAFR-rEIT) that uses a small number of electrodes and large number of rotational measurement position measurements over 360°. The results are comparable to previous rotational EIT implementations, and furthermore, the limited EIT boundary access provides space for simultaneous attachme...
Tese de doutoramento em cotutela, na area de Engenharia Biomedica, apresentada a Faculdade de Cie... more Tese de doutoramento em cotutela, na area de Engenharia Biomedica, apresentada a Faculdade de Ciencias e Tecnologia da Universidade de Coimbra e a Universite Angers - Franca
EMBEC & NBC 2017
3D cell culturing has become attractive in biology and tissue engineering laboratories as it mimi... more 3D cell culturing has become attractive in biology and tissue engineering laboratories as it mimics the natural environment for the cells to grow, differentiate and interact in all directions. To study cells and cellular interactions within 3D, cell culture requires a non-invasive, non-toxic, and high resolution imaging technique. The existing imaging techniques face challenges to image cells in 3D macro-scale environment because of the sample size, photo-bleaching or resolution requirements. Optical projection tomography (OPT) is a non-invasive 3D imaging technique for samples in the range of 1-10 mm. It works in both emission and transmission modes for fluorescence and bright-field imaging, respectively. Here, we demonstrate the use of OPT for imaging of cells and cellular materials in 3D gellan gum hydrogel. Fluorescence projection images showed alive and dead human lung fibroblast cells encapsulated in hydrogel. The mineralized extracellular matrix secreted by the human adipose stem cells in the hydrogel was evenly distributed throughout the sample and analyzable in 3D volume.
Scientific Reports
Assessing cell morphology and function, as well as biomaterial performance in cell cultures, is o... more Assessing cell morphology and function, as well as biomaterial performance in cell cultures, is one of the key challenges in cell biology and tissue engineering (TE) research. In TE, there is an urgent need for methods to image actual three-dimensional (3D) cell cultures and access the living cells. This is difficult using established optical microscopy techniques such as wide-field or confocal microscopy. To address the problem, we have developed a new protocol using Optical Projection Tomography (OPT) to extract quantitative and qualitative measurements from hydrogel cell cultures. Using our tools, we demonstrated the method by analyzing cell response in three different hydrogel formulations in 3D with 1.5 mm diameter samples of: gellan gum (GG), gelatin functionalized gellan gum (gelatin-GG), and Geltrex. We investigated cell morphology, density, distribution, and viability in 3D living cells. Our results showed the usability of the method to quantify the cellular responses to bi...
Measurement Science and Technology
Electrical impedance tomography (EIT) is an imaging method that could become a valuable tool in m... more Electrical impedance tomography (EIT) is an imaging method that could become a valuable tool in multimodal applications. One challenge in simultaneous multimodal imaging is that typically the EIT electrodes cover a large portion of the object surface. This paper investigates the feasibility of rotational EIT (rEIT) in applications where electrodes cover only a limited angle of the surface of the object. In the studied rEIT, the object is rotated a full 360° during a set of measurements to increase the information content of the data. We call this approach limited angle full revolution rEIT (LAFR-rEIT). We test LAFR-rEIT setups in two-dimensional geometries with computational and experimental data. We use up to 256 rotational measurement positions, which requires a new way to solve the forward and inverse problem of rEIT. For this, we provide a modification, available for EIDORS, in the supplementary material. The computational results demonstrate that LAFR-rEIT with eight electrodes produce the same image quality as conventional 16-electrode rEIT, when data from an adequate number of rotational measurement positions are used. Both computational and experimental results indicate that the novel LAFR-rEIT provides good EIT with setups with limited surface coverage and a small number of electrodes.
Scientific Reports
This study focuses on improving the reconstruction process of the brightfield optical projection ... more This study focuses on improving the reconstruction process of the brightfield optical projection tomography (OPT). OPT is often described as the optical equivalent of X-ray computed tomography, but based on visible light. The detection optics used to collect light in OPT focus on a certain distance and induce blurring in those features out of focus. However, the conventionally used inverse Radon transform assumes an absolute focus throughout the propagation axis. In this study, we model the focusing properties of the detection by coupling Gaussian beam model (GBM) with the Radon transform. The GBM enables the construction of a projection operator that includes modeling of the blurring caused by the light beam. We also introduce the concept of a stretched GBM (SGBM) in which the Gaussian beam is scaled in order to avoid the modeling errors related to the determination of the focal plane. Furthermore, a thresholding approach is used to compress memory usage. We tested the GBM and SGBM...
Biochimica et Biophysica Acta (BBA) - Molecular Cell Research
Phasor-assisted Metal Induced Energy Transfer-Fluorescence Lifetime Imaging Microscopy (MIET-FLIM... more Phasor-assisted Metal Induced Energy Transfer-Fluorescence Lifetime Imaging Microscopy (MIET-FLIM) nanoscopy is introduced as a powerful tool for functional cell biology research. Thin metal substrates can be used to obtain axial super resolution via nanoscale distance-dependent MIET from fluorescent dyes towards a nearby metal layer, thereby creating fluorescence lifetime contrast between dyes located at different nanoscale distance from the metal. Such data can be used to achieve axially super resolved microscopy images, a process known as MIET-FLIM nanoscopy. Suitability of the phasor approach in MIET-FLIM nanoscopy is first demonstrated using nanopatterned substrates, and furthermore applied to characterize the distance distribution of the epithelial basal membrane of a biological cell from the gold substrate. The phasor plot of an entire cell can be used to characterize the full Förster resonance energy transfer (FRET) trajectory as a large distance heterogeneity within the sensing range of about 100 nm from the metal surface is present due to the extended shape of cell with curvatures. In contrast, the different proteins of nuclear lamina show strong confinement close to the nuclear envelope in nanoscale. We find the lamin B layer resides in average at shorter distances from the gold surface compared to the lamin A/C layer located in more extended ranges. This and the observed heterogeneity of the protein layer thicknesses suggests that A- and B-type lamins form distinct networks in the nuclear lamina. Our results provide detailed insights for the study of the different roles of lamin proteins in chromatin tethering and nuclear mechanics.
Physics in Medicine & Biology
Solving the fluorophore distribution in a tomographic setting has been difficult because of the l... more Solving the fluorophore distribution in a tomographic setting has been difficult because of the lack of physically meaningful and computationally applicable propagation models. This study concentrates on the direct modelling of fluorescence signals in optical projection tomography (OPT), and on the corresponding inverse problem. The reconstruction problem is solved using emission projections corresponding to a series of rotational imaging positions of the sample. Similarly to the bright field OPT bearing resemblance with the transmission x-ray computed tomography, the fluorescent mode OPT is analogous to x-ray fluorescence tomography (XFCT). As an improved direct model for the fluorescent OPT, we derive a weighted Radon transform based on the XFCT literature. Moreover, we propose a simple and fast iteration scheme for the slice-wise reconstruction of the sample. The developed methods are applied in both numerical experiments and inversion of fluorescent OPT data from a zebrafish embryo. The results demonstrate the importance of propagation modelling and our analysis provides a flexible modelling framework for fluorescent OPT that can easily be modified to adapt to different imaging setups. PAPER Original content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence.
Nanoscale
Smart materials can significantly alter their mechanical, thermal or electromagnetic properties, ... more Smart materials can significantly alter their mechanical, thermal or electromagnetic properties, in response to external stimuli. They have enabled progress in many areas, including drug delivery, self-healing materials for coating...
Physics in medicine and biology, Dec 29, 2017
Laser speckle contrast imaging (LSCI) is a non-invasive microvascular blood flow assessment techn... more Laser speckle contrast imaging (LSCI) is a non-invasive microvascular blood flow assessment technique with good temporal and spatial resolution. Most LSCI systems, including commercial devices, can perform only qualitative blood flow evaluation, which is a major limitation of this technique. There are several factors that prevent the utilization of LSCI as a quantitative technique. Among these factors, we can highlight the effect of static scatterers. The goal of this work was to study the influence of differences in static and dynamic scatterer concentration on laser speckle correlation and contrast. In order to achieve this, a laser speckle prototype was developed and tested using an optical phantom with various concentrations of static and dynamic scatterers. It was found that the laser speckle correlation could be used to estimate the relative concentration of static/dynamic scatterers within a sample. Moreover, the speckle correlation proved to be independent of the dynamic sca...
ABSTRACT Hydrogels have many applications in tissue engineering (TE) research due to their simila... more ABSTRACT Hydrogels have many applications in tissue engineering (TE) research due to their similarities to soft tissue. Benefits of using optical projection tomography (OPT) and selective plane illumination microscopy (SPIM) optical techniques for image 3D hydrogel structures are discussed.
Langmuir : the ACS journal of surfaces and colloids, May 3, 2016
The microstructure and permeability are crucial factors for the development of hydrogels for tiss... more The microstructure and permeability are crucial factors for the development of hydrogels for tissue engineering, since they influence cell nutrition, penetration and proliferation. The currently available imaging methods able to characterize hydrogels have many limitations. They often require sample drying and other destructive processing, which can change hydrogel structure, or they have limited imaging penetration depth. In this work, we show for the first time an alternative non-destructive method, based on optical projection tomography (OPT) imaging, to characterize hydrated hydrogels without the need of sample processing. As proof of concept we used gellan gum (GG) hydrogels obtained by several crosslinking methods. Transmission mode OPT was used to analyse image microtextures and emission mode OPT to study mass transport. Differences in hydrogels structure related to different types of crosslinking and between modified and native GG were found through the acquired Haralick'...
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Papers by Edite Figueiras