Automatic pseudo-coloring approaches to improve visual perception and contrast in polarimetric images of biological tissues.

Imaging polarimetry methods have proved their suitability to enhance the image contrast between tissues and structures in organic samples, or even to reveal structures hidden in regular intensity images. These methods are nowadays used in a wide range of biological applications, as for the early diagnosis of different pathologies. To include the discriminatory potential of different polarimetric observables in a single image, a suitable strategy reported in literature consists in associating different observables to different color channels, giving rise to pseudo-colored images helping the visualization of different tissues in samples. However, previous reported polarimetric based pseudo-colored images of tissues are mostly based on simple linear combinations of polarimetric observables whose weights are set ad-hoc, and thus, far from optimal approaches. In this framework, we propose the implementation of two pseudo-colored methods. One is based on the Euclidean distances of actual values of pixels and an average value taken over a given region of interest in the considered image. The second method is based on the likelihood for each pixel to belong to a given class. Such classes being defined on the basis of a statistical model that describes the statistical distribution of values of the pixels in the considered image. The methods are experimentally validated on four different biological samples, two of animal origin and two of vegetal origin. Results provide the potential of the methods to be applied in biomedical and botanical applications.

Unraveling the physical information of depolarizers.

The link between depolarization measures and physical nature and structure of material media inducing depolarization is nowadays an open question. This article shows how the joint use of two complementary sets of depolarizing metrics, namely the Indices of polarimetric purity and the Components of purity, are sufficient to completely describe the integral depolarizing properties of a sample. Based on a collection of illustrative and representative polarimetric configurations, a clear and meaningful physical interpretation of such metrics is provided, thus extending the current tools and comprehension for the study and analysis of the depolarizing properties of material media. This study could be of interest to those users dealing with depolarization or depolarizing samples.

Polarimetric data-based model for tissue recognition.

We highlight the potential of a predictive optical model method for tissue recognition, based on the statistical analysis of different polarimetric indicators that retrieve complete polarimetric information (selective absorption, retardance and depolarization) of samples. The study is conducted on the experimental Mueller matrices of four biological tissues (bone, tendon, muscle and myotendinous junction) measured from a collection of 157 ex-vivo chicken samples. Moreover, we perform several non-parametric data distribution analyses to build a logistic regression-based algorithm capable to recognize, in a single and dynamic measurement, whether a sample corresponds (or not) to one of the four different tissue categories.

Polarimetric imaging microscopy for advanced inspection of vegetal tissues.

Optical microscopy techniques for plant inspection benefit from the fact that at least one of the multiple properties of light (intensity, phase, wavelength, polarization) may be modified by vegetal tissues. Paradoxically, polarimetric microscopy although being a mature technique in biophotonics, is not so commonly used in botany. Importantly, only specific polarimetric observables, as birefringence or dichroism, have some presence in botany studies, and other relevant metrics, as those based on depolarization, are underused. We present a versatile method, based on a representative selection of polarimetric observables, to obtain and to analyse images of plants which bring significant information about their structure and/or the spatial organization of their constituents (cells, organelles, among other structures). We provide a thorough analysis of polarimetric microscopy images of sections of plant leaves which are compared with those obtained by other commonly used microscopy techniques in plant biology. Our results show the interest of polarimetric microscopy for plant inspection, as it is non-destructive technique, highly competitive in economical and time consumption, and providing advantages compared to standard non-polarizing techniques.

Depolarization metric spaces for biological tissues classification.

Classification of tissues is an important problem in biomedicine. An efficient tissue classification protocol allows, for instance, the guided-recognition of structures through treated images or discriminating between healthy and unhealthy regions (e.g., early detection of cancer). In this framework, we study the potential of some polarimetric metrics, the so-called depolarization spaces, for the classification of biological tissues. The analysis is performed using 120 biological ex vivo samples of three different tissues types. Based on these data collection, we provide for the first time a comparison between these depolarization spaces, as well as with most commonly used depolarization metrics, in terms of biological samples discrimination. The results illustrate the way to determine the set of depolarization metrics which optimizes tissue classification efficiencies. In that sense, the results show the interest of the method which is general, and which can be applied to study multiple types of biological samples, including of course human tissues. The latter can be useful for instance, to improve and to boost applications related to optical biopsy.

Influence of temporal averaging in the performance of a rotating retarder imaging Stokes polarimeter.

We study the optimum operating conditions for a rotating retarder fixed polarizer (RRFP) when the measurements are not quasi-instantaneous but time-averaged. We obtain the optimum retardance and retarder orientations as a function of the integrated angle interval. We also study how the increase in the number of time-averaged measurements leads to a better equally weighted variance (EWV) value, and thus, to a better performance of the polarimeter in terms of noise amplification for the case of additive noise. Two different analyzers configurations are studied in this work: uniformly spaced retarder angles and when measurements are taken at optimum angles (non-uniformly spaced angles). We also consider the case of polychromatic illumination. We discuss the best measurement conditions in terms of the signal-to-noise ratio depending on whether there is a fixed or a limited amount of photons per measurement.

Depolarizing metrics for plant samples imaging.

Optical methods, as fluorescence microscopy or hyperspectral imaging, are commonly used for plants visualization and characterization. Another powerful collection of optical techniques is the so-called polarimetry, widely used to enhance image contrast in multiple applications. In the botanical applications framework, in spite of some works have already highlighted the depolarizing print that plant structures left on input polarized beams, the potential of polarimetric methods has not been properly exploited. In fact, among the few works dealing with polarization and plants, most of them study light scattered by plants using the Degree of Polarization (DoP) indicator. Other more powerful depolarization metrics are nowadays neglected. In this context, we highlight the potential of different depolarization metrics obtained using the Mueller matrix (MM) measurement: the Depolarization Index and the Indices of Polarimetric Purity. We perform a qualitative and quantitative comparison between DoP- and MM-based images by studying a particular plant, the Hedera maroccana. We show how Mueller-based metrics are generally more suitable in terms of contrast than DoP-based measurements. The potential of polarimetric measurements in the study of plants is highlighted in this work, suggesting they can be applied to the characterization of plants, plant taxonomy, water stress in plants, and other botanical studies.

Generation of reconfigurable optical traps for microparticles spatial manipulation through dynamic split lens inspired light structures.

We present an experimental method, based on the use of dynamic split-lens configurations, useful for the trapping and spatial control of microparticles through the photophoretic force. In particular, the concept of split-lens configurations is exploited to experimentally create customized and reconfigurable three-dimensional light structures, in which carbon coated glass microspheres, with sizes in a range of 63-75 µm, can be captured. The generation of light spatial structures is performed by properly addressing phase distributions corresponding to different split-lens configurations onto a spatial light modulator (SLM). The use of an SLM allows a dynamic variation of the light structures geometry just by modifying few control parameters of easy physical interpretation. We provide some examples in video format of particle trapping processes. What is more, we also perform further spatial manipulation, by controlling the spatial position of the particles in the axial direction, demonstrating the generation of reconfigurable three-dimensional photophoretic traps for microscopic manipulation of absorbing particles.

Polarimetric imaging of biological tissues based on the indices of polarimetric purity.

We highlight the interest of using the indices of polarimetric purity (IPPs) to the inspection of biological tissues. The IPPs were recently proposed in the literature and they result in a further synthetization of the depolarizing properties of samples. Compared with standard polarimetric images of biological samples, IPP-based images lead to larger image contrast of some biological structures and to a further physical interpretation of the depolarizing mechanisms inherent to the samples. In addition, unlike other methods, their calculation do not require advanced algebraic operations (as is the case of polar decompositions), and they result in 3 indicators of easy implementation. We also propose a pseudo-colored encoding of the IPP information that leads to an improved visualization of samples. This last technique opens the possibility of tailored adjustment of tissues contrast by using customized pseudo-colored images. The potential of the IPP approach is experimentally highlighted along the manuscript by studying 3 different ex-vivo samples. A significant image contrast enhancement is obtained by using the IPP-based methods, compared to standard polarimetric images.

Synthesis and characterization of depolarizing samples based on the indices of polarimetric purity.

In this work, we discuss the interest of using the indices of polarimetric purity (IPPs) as a criterion for the characterization and classification of depolarizing samples. We prove how differences in the depolarizing capability of samples, not seen by the commonly used depolarization index PΔ, are identified by the IPPs. The above-stated result is analyzed from a theoretical point of view and experimentally verified through a set of polarimetric measurements. We show how the approach presented here can be useful in easily synthetizing depolarizing samples with controlled depolarizing features, just by properly combining low-cost fully polarizing elements (such as linear retarders or polarizers).

Polarization gating based on Mueller matrices.

We present mathematical formulas generalizing polarization gating (PG) techniques. PG refers to a collection of imaging methods based on the combination of different controlled polarization channels. In particular, we show how using the measured Mueller matrix (MM) of a sample, a widespread number of PG configurations can be evaluated just from analytical expressions based on the MM coefficients. We also show the interest of controlling the helicity of the states of polarization used for PG-based metrology, as this parameter has an impact in the image contrast of samples. In addition, we highlight the interest of combining PG techniques with tools of data analysis related to the MM formalism, such as the well-known MM decompositions. The method discussed in this work is illustrated with the results of polarimetric measurements done on artificial phantoms and real ex-vivo tissues.