Diatoms are one of the largest groups of microalgae present in marine, freshwater and transitional environments and their reactivity to environmental changes makes them suitable to be employed as biomarkers for monitoring tasks. Anyway, their presence in a large number of species makes it arduous to perform diatoms taxonomy during monitoring tasks considering that, to date, analysis is conducted by marine biologists on the basis of their own experience and, hence, in a subjective way. Hence, the need for automatic and objective methodologies for the identification and classification of diatoms samples rises. Research efforts in the field of Computer Vision led to a plethora of highly effective deep learning strategies surpassing human capabilities for image classification, as showed in the recent Imagenet challenge editions where they were initially introduced. Despite the very promising results of the proposed solutions, the difficulty arises to determine which technique is most suitable among them for real tasks and in particular for diatoms classification. This work proposes an end-to-end pipeline for automatic recognition of diatoms, acquired by means of holographic microscopy in water samples, employing deep learning techniques. In particular the most recently introduced Convolution Neural Networks (CNNs) architectures have been deeply investigated and compared in order to highlight the pros and cons of each of them. Moreover, in order to feed the CNNs training stages with a suitable amount of labeled data, a strategy to build a synthetic dataset, starting from a single image per class available from commercial glass slides specifically prepared for taxonomy purposes, is introduced. Besides, models ensembling strategies, in order to improve the single model scores, have been exploited. Finally, the proposed approach has been validated employing a dataset built up of holographic images of diatoms sampled in natural water bodies.
Microplastics are worrisome water pollutants that are more and more spread in deep sea and coastal waters. Plastic items can take decades to biodegrade, have the potential to affect the food chain and are harmful to marine life. Hence, there is the urgent need to define protocols and to create reliable tools to map the presence of microplastics in heterogeneous liquid samples. However, well established protocols and tools to identify microplastics in water have not been proposed yet. Here we investigate this class of objects by means of coherent imaging, in particular relying on Digital Holography (DH) microscopy. We provide a DH characterization of the “plastic” class that can be used as a global identifier independently on the plastic material under analysis. We probe microplastics of various materials through our DH microscope and show that the phase contrast map of microplastics can be used to define a fingerprint for the microplastics population. Thanks to the DH flexible refocusing, volumetric counting of microplastics in flow is feasible by DH with high-throughput. Remarkably, field-deployable, cost effective DH microscopes exist that can bring the DH characterization potential out of the lab for in situ environmental monitoring.
Learning to automatically recognize objects in the real world is a very important and stimulating challenge. This work deals with the problem of detecting aluminium profiles within images, using hierarchical representations such as those based on deep learning methods. The use of regional CNN, a conceptually simple, flexible, and general framework for object instance segmentation, allows to exceed the previous state-of-the-art results. This approach efficiently detects objects in an image while simultaneously generating a high-quality segmentation mask for each instance. Neural network training uses ResNet networks of depth 50 or 101 layers. In particular, the training dataset consists of synthetic data generated by CAD files. The Dataset creation process is fundamental: experimental results show that trivial datasets lead to poor detection performance. A rich dataset, instead, including more complex images, allows the network to learn more and better guaranteeing excellent results. How to get more data, if you do not have more data? To get more data, we just need to make minor alterations such as flips, scale or rotations to existing dataset. This process is known as Data augmentation. The performance of the proposed system strongly depends on the dataset used for training and on the backbone architecture used. This why, adopting a strategy that generates a priori a very large dataset the time required to create the annotation file grows almost exponentially. The validation and test dataset, on the other hand, consists of real images captured by cameras. The distinctiveness of this work consists to train a deep neural network with synthetic data (aluminium CAD files) and verify if it on real data. Experiments show that the implementation of architecture, as described above, leads to good performance in automatic detection and classification. Future work will be addressed to improve the network training process together with the architecture, the algorithms and the dataset creation process. The latter is proved to be fundamental for the balance and optimization of the whole process. The way is to develop not much augmented datasets focusing on online data augmentation during network training.
The identification and classification of biological samples is high-demanded in biomedical imaging for diagnostic purposes. Among all imaging modalities, digital holography has gained credits as a powerful solutions, thanks to its ability to perform full-field and label –free quantitative phase imaging. On the other hand, machine learning is nowadays the most used approach for classification purposes. The robustness and the accuracy of the classification depend of the features used for the training step. Therefore, the identification of micro-organism becomes strictly related to the features that can be extracted from their images. In other word, the more the image contains information, the higher the possibility of extracting highly distinctive descriptors to differentiate biological phenotypes. Digital holography can be considered one of the richest in terms of information content due to the fact that a single digital hologram encode both amplitude and phase information about the imaged cells. This opens the way to improve the features extraction, thus making more accurate the classification step. In this paper we analyze a test case by using a holographic image dataset for classification, by extracting unique features that can be solely obtained by holographic images.
Nowadays, digital holography can be considered as one of the most powerful imaging modality in several research fields, from the 3D imaging for display purposes to quantitative phase image in microscopy and microfluidics. At the same time, machine learning in imaging applications has been literally reborn to the point of being considered the most exploited field by optical imaging researchers. In fact, the use of deep convolutional neural networks has permitted to achieve impressive results in the classification of biological samples obtained by holographic imaging, as well as for solving inverse problems in holographic microscopy. Definitely, machine learning approaches in digital holography has been used mainly to improve the performance of the imaging tool. Here we show a reverse modality in which holographic imaging boosts the performance of machine leaning algorithms. In particular, we identify several descriptors solely related to the type of data to be classified, i.e. the holographic image. We provide some case studies which demonstrate how the holographic imaging can improve the performance of a plain classifier.
Micro-plastics dispersion in water is one of the major global threats due to the potential of plastic items to affect the food chain and reproduction of marine organisms. However, reliable and automatic recognition of micro-plastic in water is still an unmatched goal. Here we identify micro-plastics in water samples through digital holography microscopy combined to machine learning. We exploit the rich content of information of the holographic signature to design new distinctive features that specifically characterize micro-plastics and allow distinguishing them from marine plankton of comparable size. We use these features to train a plain support vector machine, remarkably improving its performance. Thus, we obtain a very accurate classifier using a simple machine learning approach, which does not require a large amount of training data and identifies micro-plastics of various morphology and optical properties over a wide range of characteristic scales. This is a first mandatory step to develop sensor networks to map the distribution of micro-plastics in water and their flows.
A variety of optical investigation methods applied to paintings are, by now, an integral part of the repair process, both to
plan the restoration intervention and to monitor its various phases. Among them infrared reflectography in wide-band
modality is traditionally employed in non-invasive diagnostics of ancient paintings to reveal features underlying the
pictorial layer thanks to transparency characteristics to NIR radiation of most of the materials composing the paints.
This technique was improved with the introduction of the multi-spectral modality that consists in acquiring the radiation
back scattered from the painting into narrow spectral bands. The technology, widely used in remote sensing applications
such as satellite or radar imaging, has only recently gained importance in the field of artwork conservation thanks to the
varied reflectance and transmittance of pigments over this spectral region.
In this work we present a scanning device for multi-NIR spectral imaging of paintings, based on contact-less and singlepoint
measurement of the reflectance of painted surfaces. The back-scattered radiation is focused on square-shaped fiber
bundle that carries the light to an array of 16 photodiodes equipped with pass-band filters so to cover the NIR spectral
range from 900 to 2500 nm. In particular, we describe the last instrument upgrade that consists in the addition of an
autofocus system that keeps the optical head perfectly focused during the scanning. The output of the autofocus system
can be used as a raw map of the painting shape.
Surface topography is very important for many applications. Today the most used techniques on artworks and stone artifacts
require long acquisition times and invasive interventions. For this reason, here a non-contact device improved in portability
is described. It can acquire wide areas in short times, so it is suitable for topography reconstruction with spatial resolution
of some tens of micrometers.
The starting point is a commercial conoscopic probe, the Optimet Conoline, that is able to reconstruct the depth profile
of a surface line probed by a built-in laser. Its accuracy and acquisition speed are as high as to return wide measured areas
in short times; its resolution permits fine details reproduction. Low interference with the artwork, high portability and low
response to environmental noise are the ingredients for the instrumental setup.
In this paper we present a scanning device for multispectral imaging of paintings in the 380-800 nm spectral region; the
system is based on a spectrophotometer for contact-less single-point measurements of the spectral reflectance with 10
nm resolution. Two orthogonal XY translation stages allow to scan up to 1,5 m2 with spatial resolution up to 8 dots/mm.
As an application we present the results of the measurements carried out on Ritratto Trivulzio by Antonello da Messina
and Madonna in gloria tra Santi by Andrea Mantegna. Besides spectra comparison also multivariate image analyses
(MIA) have been performed by considering the multi-spectral images as three-way data set.
In order to point out the slight spectral differences of two areas of a painting we analyzed its multispectral data cube by
means of the Principal Component Analysis (PCA) and the K-Nearest-Neighbouring Cluster Analysis (KNN).
KEYWORDS: Scanners, Infrared imaging, Near infrared, Light sources and illumination, Infrared radiation, Sensors, Principal component analysis, Transparency, Diagnostics, Head
A variety of scientific investigation methods applied to paintings are, by now, an integral part of the repair process, both
to plan the restoration intervention and to monitor its various phases. Optical techniques are widely diffused and
extremely well received in the field of painting diagnostics because of their effectiveness and safety. Among them
infrared reflectography is traditionally employed in non-destructive diagnostics of ancient paintings to reveal features
underlying the pictorial layer thanks to transparency characteristics to NIR radiation of the materials composing the
paints.
High-resolution reflectography was introduced in the 90s at the Istituto Nazionale di Ottica Applicata, where a prototype
of an innovative scanner was developed, working in the 900-1700 nm spectral range. This technique was recently
improved with the introduction of an optical head, able to acquire simultaneously the reflectogram and the color image,
perfectly superimposing.
In this work we present a scanning device for multi-spectral IR reflectography, based on contact-less and single-point
measurement of the reflectance of painted surfaces. The back-scattered radiation is focused on square-shaped fiber
bundle that carries the light to an array of 14 photodiodes equipped with pass-band filters so to cover the NIR spectral
range from 800 to 2500 nm
The quantitative morphological analysis of a painting surface allows to evidence form defects and to study, thus, their
influence on the stability of the paint and preparatory layers, as well as of the support. Therefore a three-dimensional
survey can be very useful in planning the restoration intervention of a painting.
In this work we present the results of the surface analysis carried out on the painting "Ultima Cena" by Giorgio Vasari.
This panel painting is severely affected by paint film wrinkling produced as a consequence of the flood that occurred in
Florence in 1966. Our analysis, accomplished to quantify the lengthening of the paint layer with respect to the one of the
support in order to plan the restoration intervention, was performed on 25 profiles separated each by 10 cm in order to
cover the whole painting surface.
A data analysis, based on morphological filtering named "Rolling Ball" transformation, was used to evaluate the length
difference between the paint layer and the panel support along each profile.
We present a scanning device for 32-band multi-spectral imaging of paintings in the 380÷800 nm spectral region. The system is based on contact-less and single-point measurement of the spectral reflectance factor. Multi-spectral images are obtained by scanning the painted surface under investigation. An adjustment procedure was established and calibration was performed by means of a set of seven matt ceramic color tiles certified by National Physical Laboratory (UK). Colorimetric calculations were carried out in the XYZ colorimetric space, by following the CIE recommendations and choosing the D65 standard illuminant and the 1931 standard observer. Measurement campaigns were carried out on several paintings in situ and at the INOA Optical Metrology Laboratory located inside the Opificio delle Pietre Dure in Florence. As an example we report herein on the measurements carried out on the Madonna in gloria tra Santi by Andrea Mantegna, (at present in the Pinacoteque of the Castello Sforzesco in Milan). Multivariate image analyses (MIA) were performed by considering the multi-spectral images as three-way data set. The stack of detected images were unfolded in a 2D data matrix and analyzed by the conventional Principal Component Analysis (PCA).
KEYWORDS: 3D image processing, 3D modeling, Photography, Corrosion, Statistical analysis, Surface roughness, 3D metrology, Data acquisition, Image processing software, Cultural heritage
A quantitative morphological analysis of archaeological objects represents an important element for historical evaluations, artistic studies and conservation projects.
At present, a variety of contact instruments for high-resolution surface survey is available on the market, but because of their invasivity they are not well received in the field of artwork conservation. On the contrary, optical testing techniques have seen a successful growth in last few years due to their effectiveness and safety.
In this work we present a few examples of application of high-resolution 3D techniques for the survey of archaeological objects.
Measurements were carried out by means of an optical micro-profilometer composed of a commercial conoprobe mounted on a scanning device that allows a maximum sampled area of 280×280 mm2.
Measurements as well as roughness calculations were carried out on selected areas, representative of the differently degraded surface, of an ellenestic bronze statue to document the surface corrosion before restoration intervention started. Two highly-corroded ancient coins and a limestone column were surveyed to enhance the relief of inscriptions and drawings for dating purposes.
High-resolution 3D survey, beyond the faithful representation of objects, makes it possible to display the surface in an image format that can be processed by means of image processing software. The application of digital filters as well as rendering techniques easies the readability of the smallest details.
In the last few years multispectral imaging has entered the field of painting diagnostics and conservation because of its effectiveness and safety. It provides spectral and colorimetric characterization of the whole paint layer, suitable to document the conservation state of the artwork and useful in the study for the identification of pigments.
Here we present a high-resolution scanning system for 32-band multispectral imaging of paintings in the 380÷800 nm spectral region. This system is based on a fast spectrometer for contact-less single-point measures mounted on two orthogonal XY translation stages. It can scan an area of 1 m2 with a spatial resolution of 4 dots/mm and a spectral resolution of 10 nm.
Spectral reflection factor and tristimulus value measurements were carried out on coloured ceramic tiles and the results were compared with the corresponding certified values.
Multispectral analysis was performed on a few ancient paintings and spectrophotometric results are shown.
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