A cockpit of multiple measures for assessing film restoration quality

In machine vision, the idea of expressing the quality of a films by a single value is very popular. Usually this value is computed by processing a set of image features with the aim of resembling as much as pos- sible a kind of human judgment of the film quality. Since human quality assessment is a complex mech- anism involving many different perceptual aspects, we believe that such approach may scarcely provide a comprehensive analysis. Especially in the field of digital movie restoration, a single score can hardly provide reliable information about the effects of the various restoring operations. For this reason we in- troduce an alternative approach, where a set of measures, describing over time basic global and local visual properties of the film frames, is computed in an unsupervised way and delivered to expert evalu- ators for checking the restoration pipeline and results. The proposed framework can be viewed as a car or airplane cockpit , whose parameters (i.e. the computed measures) are necessary to control the machine status and performance. This cockpit, which is publicly available online, would like to support the digital restoration process and its assessment

Review and Comparison of Random Spray Retinex and of its variants STRESS and QBRIX

In this paper, we review and compare three spatial color algorithms of the Milano Retinex family: Random Spray Retinex (RSR) and its subsequent variants STRESS and QBRIX. These algorithms process the colors of any input image in line with the principles of the Retinex theory, introduced about 50 years ago by Land and McCann to explain how humans see colors. According to this theory, RSR, STRESS and QBRIX re-scale independently the color intensities of each pixel by a quantity, named local reference white, which depends on the spatial arrangement of the colors in the pixel surround. The output is a new color enhanced image that generally has a higher brightness and more visible details than the input one. RSR, STRESS and QBRIX adopt different models of spatial arrangement and implement different equations for the computation of the local reference white, so that they produce different enhanced images. We propose a comparative analysis of their performance based on numerical measures of the image brightness, details and dynamic range. In order to enable result repeatability and further comparisons, we use a set of images publicly available on the net

Evidence that Viewers Prefer Higher Frame Rate Film

High frame rate (HFR) movie-making refers to the capture and projection of movies at frame rates several times higher than the traditional 24 frames per second. This higher frame rate theoretically improves the quality of motion portrayed in movies, and helps avoid motion blur, judder and other undesirable artefacts. However, there is considerable debate in the cinema industry regarding the acceptance of HFR content given anecdotal reports of hyper-realistic imagery that reveals too much set and costume detail. Despite the potential theoretical advantages, there has been little empirical investigation of the impact of high-frame rate techniques on the viewer experience. In this study we use stereoscopic 3D content, filmed and projected at multiple frame rates (24, 48 and 60 fps), with shutter angles ranging from 90 degrees to 358 degrees, to evaluate viewer preferences. In a paired-comparison paradigm we assessed preferences along a set of five attributes (realism, motion smoothness, blur/clarity, quality of depth and overall preference). The resulting data show a clear preference for higher frame rates, particularly when contrasting 24 fps with 48 or 60 fps. We found little impact of shutter angle on viewers’ choices, with the exception of one measure (motion smoothness) for one clip type. These data are the first empirical evidence of the advantages afforded by high frame rate capture and presentation in a cinema context.https://source.sheridancollege.ca/centres_sirt_works/1000/thumbnail.jp

Evaluation of the color image and video processing chain and visual quality management for consumer systems

With the advent of novel digital display technologies, color processing is increasingly becoming a key aspect in consumer video applications. Today’s state-of-the-art displays require sophisticated color and image reproduction techniques in order to achieve larger screen size, higher luminance and higher resolution than ever before. However, from color science perspective, there are clearly opportunities for improvement in the color reproduction capabilities of various emerging and conventional display technologies. This research seeks to identify potential areas for improvement in color processing in a video processing chain. As part of this research, various processes involved in a typical video processing chain in consumer video applications were reviewed. Several published color and contrast enhancement algorithms were evaluated, and a novel algorithm was developed to enhance color and contrast in images and videos in an effective and coordinated manner. Further, a psychophysical technique was developed and implemented for performing visual evaluation of color image and consumer video quality. Based on the performance analysis and visual experiments involving various algorithms, guidelines were proposed for the development of an effective color and contrast enhancement method for images and video applications. It is hoped that the knowledge gained from this research will help build a better understanding of color processing and color quality management methods in consumer video

Ki67 nuclei detection and ki67-index estimation: A novel automatic approach based on human vision modeling

Background: The protein ki67 (pki67) is a marker of tumor aggressiveness, and its expression has been proven to be useful in the prognostic and predictive evaluation of several types of tumors. To numerically quantify the pki67 presence in cancerous tissue areas, pathologists generally analyze histochemical images to count the number of tumor nuclei marked for pki67. This allows estimating the ki67-index, that is the percentage of tumor nuclei positive for pki67 over all the tumor nuclei. Given the high image resolution and dimensions, its estimation by expert clinicians is particularly laborious and time consuming. Though automatic cell counting techniques have been presented so far, the problem is still open. Results: In this paper we present a novel automatic approach for the estimations of the ki67-index. The method starts by exploiting the STRESS algorithm to produce a color enhanced image where all pixels belonging to nuclei are easily identified by thresholding, and then separated into positive (i.e. pixels belonging to nuclei marked for pki67) and negative by a binary classification tree. Next, positive and negative nuclei pixels are processed separately by two multiscale procedures identifying isolated nuclei and separating adjoining nuclei. The multiscale procedures exploit two Bayesian classification trees to recognize positive and negative nuclei-shaped regions. Conclusions: The evaluation of the computed results, both through experts' visual assessments and through the comparison of the computed indexes with those of experts, proved that the prototype is promising, so that experts believe in its potential as a tool to be exploited in the clinical practice as a valid aid for clinicians estimating the ki67-index. The MATLAB source code is open source for research purposes

In vivo and in vitro analysis of RNases in Bacillus subtilis

RNA degradation is a key process in the control of gene expression in bacteria and is essential for the cell’s homeostasis of nucleotide pools. A key player is the so-called RNA degradosome, proposed to be a membrane-associated complex containing endo- and exoribunucleases, as well as glycolytic enzymes and a DEAD-box RNA helicase. It is believed that endonuclease RNase Y is central to the formation of the RNA degradosome in Bacillus subtilis, leading to recruitment of RNases PnpA, RNase J1, and RNase J2, RNA helicase CshA, as well as glycolytic enzymes enolase and phosphofructokinase occurs. RNase Y has a transmembrane helix, and is "quasi“ essential; it is also required for mRNA processing following transcription. RNase Y also interacts with the so-called Y‑complex, consisting of YaaT, YlbF, and, YmcA (RicT, RicF, RicA), which is important for RNase Y-mediated processing of mRNA. How RNase Y can operate in two different protein complexes and acts in RNA decay as well as transcription-associated processes, is unclear. In this work, I show that the RNA degradosome is quite dynamic, having RNase Y, the glycolytic enzyme enolase, and the RNA helicase CshA and PnpA as central parts strongly reacting to a block in transcription, and thus to loss of mRNA substrate, while RNase J1 and J2 as well as the glycolytic enzyme phosphofructokinase show a much weaker response and are thus likely more peripheral components. The Y-complex clearly shows diffusion within the cytosol, but also the formation of membrane-associated accumulations, dissociating when transcription is blocked. Single molecule tracking (SMT) shows that the loss of one component of the Y-complex does not strongly affect the dynamics of the other proteins, suggesting that the complex forms a flexible association rather than a 1:1:1 stoichiometry. Biochemical analyses suggest that YaaT forms a membrane-anchor for the Y-complex, although it also has a cytosolic, freely diffusing fraction. A model will be presented that the Y-complex could function as an adaptor between nucleoid-associated mRNA synthesis and membrane-associated processing and degradation. II My thesis also presents a protocol for the successful purification of membrane-associated RNase Y, as a basis for further biochemical characterization of the protein, and interaction studies. Another essential process in which RNases play a crucial role is DNA replication. In addition to the RNA primers, which are necessary for the placement of Okazaki fragments, DNA/RNA hybrids must be processed and RNA must be removed to ensure the stability of the DNA. A part of the thesis work shows that B. subtilis replication forks intimately employ two RNases of the „H“ family, DNA polymerase A and exonuclease ExoR in vivo. Recruitment appears to be based on substrate availability rather than on specific protein/protein interactions, involving redundant enzymatic activities

Change blindness: eradication of gestalt strategies

Arrays of eight, texture-defined rectangles were used as stimuli in a one-shot change blindness (CB) task where there was a 50% chance that one rectangle would change orientation between two successive presentations separated by an interval. CB was eliminated by cueing the target rectangle in the first stimulus, reduced by cueing in the interval and unaffected by cueing in the second presentation. This supports the idea that a representation was formed that persisted through the interval before being 'overwritten' by the second presentation (Landman et al, 2003 Vision Research 43149–164]. Another possibility is that participants used some kind of grouping or Gestalt strategy. To test this we changed the spatial position of the rectangles in the second presentation by shifting them along imaginary spokes (by ±1 degree) emanating from the central fixation point. There was no significant difference seen in performance between this and the standard task [F(1,4)=2.565, p=0.185]. This may suggest two things: (i) Gestalt grouping is not used as a strategy in these tasks, and (ii) it gives further weight to the argument that objects may be stored and retrieved from a pre-attentional store during this task

Pushing Light-Sheet Microscopy to Greater Depths

Light-sheet fluorescence microscopy (LSFM) has established itself as an irreplaceable imaging technique in developmental biology over the past two decades. With its emergence, the extended recording of in toto datasets of developing organisms across scales became possible. Remarkably, LSFM opened the door to new spatio-temporal domains in biology, offering cellular resolution on the one hand, and temporal resolution on the order of seconds on the other hand. As in any fluorescence microscopy technique, LSFM is also affected by image degradation at greater tissue depths. Thus far, this has been addressed by the suppression of scattered light, use of fluorophores emitting in the far red spectrum, multi-view detection and fusion, adaptive optics, as well as different illumination schemes. In this work, I investigate for the first time in vivo optical aberration reduction via refractive index matching in LSFM. Examples are shown on common model organisms as Arabidopsis thalina, Oryzias latipes, Mus musculus, as well as Drosophila. Additionally, I present a novel open-top light-sheet microscope, tailored for high-throughput imaging of mammalian samples, such as early stage mouse embryos. It is based on a three objective geometry, encompassing two opposing detection objective lenses with high light collection efficiency, and an invertedly mounted illumination lens. It bridges the spatial scale between samples by employing an extendible light-sheet illumination via a tunable acoustic gradient index lens. Both parts of this work improve the image quality across the 3D volume of specimens, paving the way for more quantitative recordings at greater tissue depths

Spatio-temporal regulation of mRNA decay revealed by a novel single-molecule dual-color imaging method

Discoveries that have been made over past decades emphasized the importance of post-transcriptional control as a means of regulating gene expression. RNA turnover is one of the key aspects of post-transcriptional control that contributes directly towards maintenance of normal cellular homeostasis. Degradation of functional messenger RNAs (mRNAs) is a tightly regulated process and its dysregulation results in either excessive or insufficient amounts of mRNAs within cells that eventually lead to a disease-associated condition. Furthermore, multiple quality control mechanisms eliminate aberrant mRNAs thereby preventing their translation into malfunctioning proteins. The realization of the importance of RNA decay pathways has fueled further research towards understanding the underlying molecular mechanisms in RNA turnover and its regulation. All protein-coding mRNAs, as well as non-coding RNAs, have distinct half-lives and are ultimately degraded. Previously, many of the factors involved in RNA decay pathways have been identified and studied. Two types of enzymes are shared among RNA decay pathways: exonucleases and endonucleases. The former are further divided into 5′-to-3′ and 3′-to-5′ degrading enzymes and their activation is often dependent on prior removal of terminal stability marks from an RNA molecule. The best-studied exonuclease is Xrn1 that degrades an RNA substrate from the 5′-end to 3′-end. On the other hand, endonucleases cleave an RNA strand to expose the resultant fragments to exonucleases, circumventing the requirement of first removing the stability marks. Most of our current appreciation of the molecular mechanisms related to the mRNA decay is attributable to the methods that involve ensemble measurements. However, these measurements often result in an averaged outcome from whole population of cells, wherein information about variability among individual cells is lost. In addition, the possibility to get information on the spatio-temporal regulation of mRNA decay is limited using ensemble methods. Hence, accurate dissection of the spatial and temporal regulation of mRNA decay requires development of a single-molecule method that preserves information on cell-to-cell variability. Single-molecule RNA imaging methods have already been used to study several aspects of the mRNA life cycle and they have helped to uncover in vivo regulations that were not possible to observe before. However, a powerful imaging method allowing for an observation of mRNA turnover in real-time at the level of single cells/molecules has been missing. During my PhD, I established a robust single-molecule imaging technique in order to characterize the spatio-temporal dynamics of RNA turnover within its cellular context. I engineered an mRNA reporter that contains viral tandem pseudo-knots placed between PP7 and MS2 stem-loops. These orthogonal stem-loops can be labeled with spectrally distinct fluorescent proteins. In addition, the viral pseudo-knots block Xrn1-mediated degradation resulting in stabilization of the reporter’s 3′-degradation intermediate that is otherwise inherently instable. This stabilized 3′-end contains only the MS2 stem-loop region. Thus, intact mRNAs are labeled with both fluorophores, while incompletely degraded mRNA fragments are labeled only with a single fluorophore. I used the amounts and positions of intact mRNAs and stabilized 3′-ends as readout of mRNA degradation. Therefore, this technique is called 3(Three)′-RNA End Accumulation during Turnover (TREAT). I applied TREAT to monitor the fates of mRNAs in single fixed and living mammalian cells. Using this method, I measured the kinetics and cell-to-cell variability of mRNA decay in fixed cells. The nuclear export rates and cytoplasmic mRNA half-lives showed that individual degradation events occur independently within the cytoplasm suggesting that there is no burst in mRNA degradation. In addition, I found that transcripts, as well as degradation intermediates, are dispersed throughout cytoplasm and are not enriched within processing bodies in living cells. Imaging of an mRNA biosensor targeted for an endonucleolytic cleavage by the RNA-induced silencing complex (RISC) showed that slicing can be observed in real-time in cytoplasm of living cells but does not occur in nucleus. The slicing events were found to have no spatial preference with respect to the distance from the nucleus. In addition to the rate of synthesis and the rate of turnover, the levels of mRNAs were found to be affected by the rate of translation as well. Indeed, I have also observed that inhibition of translation by several compounds increases mRNA stability, suggesting that the processes of mRNA degradation and translation are globally interconnected. The cross-talk among three processes central to the mRNA life cycle, transcription, degradation and translation, is becoming increasingly apparent. However, further research is required to obtain a detailed understanding of the molecular interplays in eukaryotic cells. As TREAT system visualizes mRNA from its synthesis in the nucleus through export to degradation in cytoplasm, I anticipate that this methodology will provide a framework for investigating the entire life history of individual mRNAs in single cells