Methods for Improving the Tone Mapping for Backward Compatible High Dynamic Range Image and Video Coding

International audienceBackward compatibility for high dynamic range image and video compression forms one of the essential requirements in the transition phase from low dynamic range (LDR) displays to high dynamic range (HDR) displays. In a recent work [1], the problems of tone mapping and HDR video coding are originally fused together in the same mathematical framework, and an optimized solution for tone mapping is achieved in terms of the mean square error (MSE) of the logarithm of luminance values. In this paper, we improve this pioneer study in three aspects by considering its three shortcomings. First, the proposed method [1] works over the logarithms of luminance values which are not uniform with respect to Human Visual System (HVS) sensitivity. We propose to use the perceptually uniform luminance values as an alternative for the optimization of tone mapping curve. Second, the proposed method [1] does not take the quality of the resulting tone mapped images into account during the formulation in contrary to the main goal of tone mapping research. We include the LDR image quality as a constraint to the optimization problem and develop a generic methodology to compromise the trade-off between HDR and LDR image qualities for coding. Third, the proposed method [1] simply applies a low-pass filter to the generated tone curves for video frames to avoid flickering during the adaptation of the method to the video. We instead include an HVS based flickering constraint to the optimization and derive a methodology to compromise the trade-off between the rate-distortion performance and flickering distortion. The superiority of the proposed methodologies is verified with experiments on HDR images and video sequences

Learning Clustering-Based Linear Mappings for Quantization Noise Removal

International audienceThis paper describes a novel scheme to reduce the quantization noise of compressed videos and improve the overall coding performances. The proposed scheme first consists in clustering noisy patches of the compressed sequence. Then, at the encoder side, linear mappings are learned for each cluster between the noisy patches and the corresponding source patches. The linear mappings are then transmitted to the decoder where they can be applied to perform de-noising. The method has been tested with the HEVC standard, leading to a bitrate saving of up to 9.63%

Development and characterization of two new tools for plant genetic engineering: A CRISPR/Cas12a-based mutagenesis system and a PhiC31-based gene switch

Tesis por compendio[ES] La mejora genética vegetal tiene como objetivo la obtención de plantas con rasgos mejorados o características novedosas que podrían ayudar a superar los objetivos de sostenibilidad. Para este fin, la biotecnología vegetal necesita incorporar nuevas herramientas de ingeniería genética que combinen una mayor precisión con una mayor capacidad de mejora. Las herramientas de edición genética recientemente descubiertas basadas en la tecnología CRISPR/Cas9 han abierto el camino para modificar los genomas de las plantas con una precisión sin precedentes. Por otro lado, los nuevos enfoques de biología sintética basados en la modularidad y la estandarización de los elementos genéticos han permitido la construcción de dispositivos genéticos cada vez más complejos y refinados aplicados a la mejora genética vegetal. Con el objetivo final de expandir la caja de herramientas biotecnológicas para la mejora vegetal, esta tesis describe el desarrollo y la adaptación de dos nuevas herramientas: una nueva endonucleasa específica de sitio (SSN) y un interruptor genético modular para la regulación de la expresión transgénica. En una primera parte, esta tesis describe la adaptación de CRISPR/Cas12a para la expresión en plantas y compara la eficiencia de las variantes de Acidaminococcus (As) y Lachnospiraceae (Lb) Cas12a con Streptococcus pyogens Cas9 (SpCas9) descritos anteriormente en ocho loci de Nicotiana benthamiana usando expresión transitoria. LbCas12a mostró la actividad de mutagénesis promedio más alta en los loci analizados. Esta actividad también se confirmó en experimentos de transformación estable realizados en tres plantas modelo diferentes, a saber, N. benthamiana, Solanum lycopersicum y Arabidopsis thaliana. Para este último, los efectos mutagénicos colaterales fueron analizados en líneas segregantes sin la endonucleasa Cas12a, mediante secuenciación del genoma descartándose efectos indiscriminados. En conjunto, los resultados muestran que LbCas12a es una alternativa viable a SpCas9 para la edición genética en plantas. En una segunda parte, este trabajo describe un interruptor genético reversible destinado a controlar la expresión génica en plantas con mayor precisión que los sistemas inducibles tradicionales. Este interruptor, basado en el sistema de recombinación del fago PhiC31, fue construido como un dispositivo modular hecho de partes de ADN estándar y diseñado para controlar el estado transcripcional (encendido o apagado) de dos genes de interés mediante la inversión alternativa de un elemento regulador central de ADN. El estado del interruptor puede ser operado externa y reversiblemente por la acción de los actuadores de recombinación y su cinética, memoria y reversibilidad fueron ampliamente caracterizados en experimentos de transformación transitoria y estable en N. benthamiana. En conjunto, esta tesis muestra el diseño y la caracterización funcional de herramientas para la ingeniería del genómica y biología sintética de plantas que ahora ha sido completada con el sistema de edición genética CRISPR/Cas12a y un interruptor genético reversible y biestable basado en el sistema de recombinación del fago PhiC31.[CA] La millora genètica vegetal té com a objectiu l'obtenció de plantes amb trets millorats o característiques noves que podrien ajudar a superar els objectius de sostenibilitat. Amb aquesta finalitat, la biotecnologia vegetal necessita incorporar noves eines d'enginyeria genètica que combinen una major precisió amb una major capacitat de millora. Les eines d'edició genètica recentment descobertes basades en la tecnologia CRISPR/Cas9 han obert el camí per modificar els genomes de les plantes amb una precisió sense precedents. D'altra banda, els nous enfocaments de biologia sintètica basats en la modularitat i l'estandardització dels elements genètics han permès la construcció de dispositius genètics cada vegada més complexos i sofisticats aplicats a la millora genètica vegetal. Amb l'objectiu final d'expandir la caixa d'eines biotecnològiques per a la millora vegetal, aquesta tesi descriu el desenvolupament i l'adaptació de dues noves eines: una nova endonucleasa específica de lloc (SSN) i un interruptor genètic modular per a la regulació de l'expressió transgènica . En una primera part, aquesta tesi descriu l'adaptació de CRISPR/Cas12a per a l'expressió en plantes i compara l'eficiència de les variants de Acidaminococcus (As) i Lachnospiraceae (Lb) Cas12a amb la ben establida Streptococcus pyogens Cas9 (SpCas9), en vuit loci de Nicotiana benthamiana usant expressió transitòria. LbCas12a va mostrar l'activitat de mutagènesi mitjana més alta en els loci analitzats. Aquesta activitat també es va confirmar en experiments de transformació estable realitzats en tres plantes model diferents, a saber, N. benthamiana, Solanum lycopersicum i Arabidopsis thaliana. Per a aquest últim, els efectes mutagènics col·laterals van ser analitzats en línies segregants sense l'endonucleasa Cas12a, mitjançant seqüenciació completa del genoma i descartant efectes indiscriminats. En conjunt, els resultats mostren que LbCas12a és una alternativa viable a SpCas9 per a l'edició genètica en plantes. En una segona part, aquest treball descriu un interruptor genètic reversible destinat a controlar l'expressió gènica en plantes amb major precisió que els sistemes induïbles tradicionals. Aquest interruptor, basat en el sistema de recombinació del bacteriòfag PhiC31, va ser construït com un dispositiu modular fet de parts d'ADN estàndard i dissenyat per controlar l'estat transcripcional (encès o apagat) de dos gens d'interès mitjançant la inversió alternativa d'un element regulador central d'ADN. L'estat de l'interruptor pot ser operat externa i reversiblement per acció dels actuadors de recombinació i la seva cinètica, memòria i reversibilitat van ser àmpliament caracteritzats en experiments de transformació transitòria i estable en N. benthamiana. En conjunt, aquesta tesi mostra el disseny i la caracterització funcional d'eines per a l'enginyeria del genòmica i biologia sintètica de plantes que ara ha sigut completat amb el sistema d'edició genètica CRISPR/Cas12a i un interruptor genètic biestable i reversible basat en el sistema de recombinació del bacteriòfag PhiC31.[EN] Plant breeding aims to provide plants with improved traits or novel features that could help to overcome sustainability goals. To this end, plant biotechnology needs to incorporate new genetic engineering tools that combine increased precision with higher breeding power. The recently discovered genome editing tools based on CRISPR/Cas9 technology have opened the way to modify plant¿s genomes with unprecedented precision. On the other hand, new synthetic biology approaches based on modularity and standardization of genetic elements have enabled the construction of increasingly complex and refined genetic devices applied to plant breeding. With the ultimate goal of expanding the toolbox of plant breeding techniques, this thesis describes the development and adaptation to plant systems of two new breeding tools: a site-specific nuclease (SSNs), and a modular gene switch for the regulation of transgene expression. In a first part, this thesis describes the adoption of the SSN CRISPR/Cas12a for plant expression and compares the efficiency of Acidaminococcus (As) and Lachnospiraceae (Lb) Cas12a variants with the previously described Streptococcus pyogens Cas9 (SpCas9) in eight Nicotiana benthamiana loci using transient expression experiments. LbCas12a showed highest average mutagenesis activity in the loci assayed. This activity was also confirmed in stable genome editing experiments performed in three different model plants, namely N. benthamiana, Solanum lycopersicum and Arabidopsis thaliana. For the latter, off-target effects in Cas12a-free segregating lines were discarded at genomic level by deep sequencing. Collectively, the results show that LbCas12a is a viable alternative to SpCas9 for plant genome engineering. In a second part, this work describes the engineering of a new reversible genetic switch aimed at controlling gene expression in plants with higher precision than traditional inducible systems. This switch, based on the bacteriophage PhiC31 recombination system, was built as a modular device made of standard DNA parts and designed to control the transcriptional state (on or off) of two genes of interest by alternative inversion of a central DNA regulatory element. The state of the switch can be externally and reversibly operated by the action of the recombination actuators and its kinetics, memory, and reversibility were extensively characterized in N. benthamiana using both transient expression and stable transgenics. Altogether, this thesis shows the design and functional characterization of refined tools for genome engineering and synthetic biology in plants that now has been expanded with the CRISPR/Cas12a gene editing system and the phage PhiC31-based toggle switch.Bernabé Orts, JM. (2019). Development and characterization of two new tools for plant genetic engineering: A CRISPR/Cas12a-based mutagenesis system and a PhiC31-based gene switch [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/133055TESISCompendi

Scalable light field representation and coding

This Thesis aims to advance the state-of-the-art in light field representation and coding. In this context, proposals to improve functionalities like light field random access and scalability are also presented. As the light field representation constrains the coding approach to be used, several light field coding techniques to exploit the inherent characteristics of the most popular types of light field representations are proposed and studied, which are normally based on micro-images or sub-aperture-images. To encode micro-images, two solutions are proposed, aiming to exploit the redundancy between neighboring micro-images using a high order prediction model, where the model parameters are either explicitly transmitted or inferred at the decoder, respectively. In both cases, the proposed solutions are able to outperform low order prediction solutions. To encode sub-aperture-images, an HEVC-based solution that exploits their inherent intra and inter redundancies is proposed. In this case, the light field image is encoded as a pseudo video sequence, where the scanning order is signaled, allowing the encoder and decoder to optimize the reference picture lists to improve coding efficiency. A novel hybrid light field representation coding approach is also proposed, by exploiting the combined use of both micro-image and sub-aperture-image representation types, instead of using each representation individually. In order to aid the fast deployment of the light field technology, this Thesis also proposes scalable coding and representation approaches that enable adequate compatibility with legacy displays (e.g., 2D, stereoscopic or multiview) and with future light field displays, while maintaining high coding efficiency. Additionally, viewpoint random access, allowing to improve the light field navigation and to reduce the decoding delay, is also enabled with a flexible trade-off between coding efficiency and viewpoint random access.Esta Tese tem como objetivo avançar o estado da arte em representação e codificação de campos de luz. Neste contexto, são também apresentadas propostas para melhorar funcionalidades como o acesso aleatório ao campo de luz e a escalabilidade. Como a representação do campo de luz limita a abordagem de codificação a ser utilizada, são propostas e estudadas várias técnicas de codificação de campos de luz para explorar as características inerentes aos seus tipos mais populares de representação, que são normalmente baseadas em micro-imagens ou imagens de sub-abertura. Para codificar as micro-imagens, são propostas duas soluções, visando explorar a redundância entre micro-imagens vizinhas utilizando um modelo de predição de alta ordem, onde os parâmetros do modelo são explicitamente transmitidos ou inferidos no decodificador, respetivamente. Em ambos os casos, as soluções propostas são capazes de superar as soluções de predição de baixa ordem. Para codificar imagens de sub-abertura, é proposta uma solução baseada em HEVC que explora a inerente redundância intra e inter deste tipo de imagens. Neste caso, a imagem do campo de luz é codificada como uma pseudo-sequência de vídeo, onde a ordem de varrimento é sinalizada, permitindo ao codificador e decodificador otimizar as listas de imagens de referência para melhorar a eficiência da codificação. Também é proposta uma nova abordagem de codificação baseada na representação híbrida do campo de luz, explorando o uso combinado dos tipos de representação de micro-imagem e sub-imagem, em vez de usar cada representação individualmente. A fim de facilitar a rápida implantação da tecnologia de campo de luz, esta Tese também propõe abordagens escaláveis de codificação e representação que permitem uma compatibilidade adequada com monitores tradicionais (e.g., 2D, estereoscópicos ou multivista) e com futuros monitores de campo de luz, mantendo ao mesmo tempo uma alta eficiência de codificação. Além disso, o acesso aleatório de pontos de vista, permitindo melhorar a navegação no campo de luz e reduzir o atraso na descodificação, também é permitido com um equilíbrio flexível entre eficiência de codificação e acesso aleatório de pontos de vista

Discrete Wavelet Transforms

The discrete wavelet transform (DWT) algorithms have a firm position in processing of signals in several areas of research and industry. As DWT provides both octave-scale frequency and spatial timing of the analyzed signal, it is constantly used to solve and treat more and more advanced problems. The present book: Discrete Wavelet Transforms: Algorithms and Applications reviews the recent progress in discrete wavelet transform algorithms and applications. The book covers a wide range of methods (e.g. lifting, shift invariance, multi-scale analysis) for constructing DWTs. The book chapters are organized into four major parts. Part I describes the progress in hardware implementations of the DWT algorithms. Applications include multitone modulation for ADSL and equalization techniques, a scalable architecture for FPGA-implementation, lifting based algorithm for VLSI implementation, comparison between DWT and FFT based OFDM and modified SPIHT codec. Part II addresses image processing algorithms such as multiresolution approach for edge detection, low bit rate image compression, low complexity implementation of CQF wavelets and compression of multi-component images. Part III focuses watermaking DWT algorithms. Finally, Part IV describes shift invariant DWTs, DC lossless property, DWT based analysis and estimation of colored noise and an application of the wavelet Galerkin method. The chapters of the present book consist of both tutorial and highly advanced material. Therefore, the book is intended to be a reference text for graduate students and researchers to obtain state-of-the-art knowledge on specific applications

Combining CRISPR-Cas9 and Proximity Labeling to Illuminate Chromatin Composition, Organization, and Regulation

A bacterial and archaeal adaptive immune system, clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas), has recently been engineered for genome editing. This RNA-guided platform has simplified genetic manipulation and holds promise for therapeutic applications. However, off-target editing has been one of the major concerns of the commonly used Streptococcus pyogenes Cas9 (SpyCas9). Despite extensive enzyme engineering to reduce off-target editing of SpyCas9, we have turned to nature and uncovered a Cas9 ortholog from Neisseria meningitidis (Nme) with high fidelity. In the first part of my thesis, we have systematically characterized Nme1Cas9 for engineering mammalian genomes and demonstrated its high specificity by genome-wide off-targeting detection methods in vitro and in cellulo, and thus provided a new platform for accurate genome editing. Due to its flexibility, CRISPR is becoming a versatile tool not only for genome editing, but also for chromatin manipulation. These alternative applications are possible because of the programmable targeting capacity of catalytically dead Cas9 (dCas9). In the second part of my thesis, we have combined dCas9 with the engineered plant enzyme ascorbate peroxidase (APEX2) to develop a proteomic method called dCas9-APEX2 biotinylation at genomic elements by restricted spatial tagging (C-BERST). Relying on the spatially restricted, fast biotin labeling of proteins near defined genomic loci, C-BERST enables the high-throughput identification of known telomere- and centromere- associated proteomes and novel factors. Furthermore, we have extended C-BERST to map the c-fos promoter and gained new insights regarding the dynamic transcriptional regulation process. Taken together, C-BERST can advance our understanding of chromatin regulators and their roles in nuclear and chromosome biology

Mouse genome modification and investigation of episodic disease

Mouse models are essential tools for biomedical research, allowing researchers to investigate gene function and model human diseases. The mouse genome can be manipulated to ablate (“knockout”) gene function, create targeted point mutations or insert transgenes or small epitope tags. Previous gene targeting methods for creating these modifications were slow and inefficient. The arrival of CRISPR/Cas9 genome editing technology has revolutionised the production of genetically modified mice as it is easy to use, efficient and cost-effective. The research comprised in this PhD thesis explores the use of genetically modified mice to better understand human diseases, as well as developing new technologies for mouse genome editing. The first manuscript describes a phenotypic investigation of the transgenic Prrt2 knockout (Prrt2 KO) mouse. In humans, mutations in PRRT2 cause an infantile epilepsy syndrome (benign familial infantile epilepsy; BFIE) and a movement disorder in adolescence (paroxysmal kinesigenic dyskinesia; PKD). We identifed a spontaneous paroxysmal phenotype in Prrt2 KO animals, as well as premature death in HET and KO mice. Behavioural tests also revealed learning deficits and gait abnormalities in KO mice that may reflect phenotypes in homozygous patients, confirming the utility of this model for investigating PRRT2-related disorders. The second manuscript examines variants of the Streptococcus pyogenes Cas9 endonuclease (WT SpCas9) commonly used for CRISPR genome editing. Numerous Cas9 variants have recently been characterised, each recognising different PAM sequences. Most of these variants remain untested for genome editing in mice. In this study, we tested a selection of endonuclease variants (SpCas9 VQR, SpCas9 VRER, SaCas9 KKH and AsCpf1) for their ability to edit the mouse genome via mouse zygote injection, with the aim of expanding PAM targeting options. We showed that all variants are able to mutate the mouse genome, albeit with different efficiencies. We also highlighted the propensity of SaCas9 KKH to generate heterozygotes or mosaic offspring in which at least one allele remains unmodified. When editing using a ssDNA oligonucleotide repair template, SaCas9 KKH consistently left a wild type allele in correctly targeted offspring, whilst WT SpCas9 frequently mutated the other allele. This characteristic could be beneficial when targeting genes in which nullizygous mutations cause embryonic lethality, as the high efficiency of WT SpCas9 commonly prevents the production of viable offspring. With CRISPR/Cas9 technology, it has become quick and efficient to tag endogenous proteins with small epitope tags. The third manuscript in this thesis compares a series of commercially available antibodies for their efficacy to detect epitope tags on Pcdh19 HA-FLAG expression in mouse brain tissue. This model was generated within the laboratory to allow specific staining of PCDH19 for investigating protocadherin 19 girls clustering epilepsy. Of the 8 antibodies tested, only two (one HA and one FLAG) were specific for PCDH19. This data will provide guidance for researchers designing similar studies, preventing extensive optimisation of immunofluorescent staining. Together, the data presented in this thesis demonstrate the versatility and importance of mouse models for the study of gene function and neurological disease. This research provides more options for producing genetically modified mice and streamlines the downstream applications of endogenous epitope tagged genes.Thesis (Ph.D.) -- University of Adelaide, School of Biological Sciences, 201

High dynamic range imaging implementation in scene monitoring under bad illumination

Unapređenje kvaliteta slike širenjem dinamičkog opsega u poslednje vreme se intenzivno koristi. Ovo za posledicu ima prisustvo znatno više detalja na slici, što je jako bitno u većini primena. Širenje dinamičkog opsega ima svoje granice i one su definisane fizičkim limitima senzora koji se koristi, tj. ograničenjima njegovog A/D konvertora. Kada je dinamički opseg scene značajno širi od dinamičkog opsega senzora, mnogi detalji neće biti adekvatno prikazani na slici. Međutim, ukoliko senzor inherentno podržava široki dinamički opseg, jasno se može uočiti da je snimljena slika kvalitetnija od one koja se dobija sa standardnog senzora...Improving image quality by expanding the dynamic range is extensively used recently. This results in the presence of significantly more details in the picture, which is very important for most applications. Expanding the dynamic range has its limits, and they are defined by the physical limits of sensor used, i.e. the limits of its A / D converter. When the dynamic range of the scene is significantly wider than the dynamic range of the sensor, many details will not be shown properly in the picture. However, if the sensor inherently supports wide dynamic range, it can be clearly noticed that the recorded image quality is higher than the one obtained with the standard sensors..

CCR5 gene knock-out mediated TALEN technique and its effects against HIV infection on lymphocytes and macrophages

Most strains of HIV-1 use CD4 and CCR5 as receptors for cell entry. A naturally occurring CCR5 gene mutation known as CCR5-Δ32 results in CCR5 dysfunction and makes the cells resistant to HIV-1 infection. Previously, two patients who received hematopoietic stem cell transplantation which carried homozygous CCR5-Δ32 have had their HIV-1 infection functionally cured, suggesting that gene-editing targeting CCR5 could make it possible for curing HIV-1 infection. Currently, the transcription activator-like effector nucleases (TALEN) system provides the highest accuracy on gene editing with good efficiency. In this study, I aim to establish a TALEN-based gene-editing platform targeting CCR5 for HIV-1 cure. Previous publication has indicated that mRNA has more advantages than DNA when delivered to the cells. Thus, firstly in this study, I optimized electroporation delivery of mRNAs to the cells and then the protocol of in vitro transcription of mRNA. After transfecting primary T cells with TALEN mRNAs, the expression of surface CCR5 was downregulated. The disruption of the CCR5 gene was confirmed on the genomic level. After HIV-1 challenge, the CCR5 gene-edited primary T cells showed increased HIV-1 resistance. Macrophages also express CD4 and CCR5, which makes them another target of HIV-1 besides CD4+ T cells. Moreover, HIV-1-infected macrophages are more resistant to immune attack and are a key reservoir of HIV-1. Thus, I tested this TALEN system on monocytes-derived-macrophages (MDMs). After transfection of the TALEN mRNAs, the surface CCR5 expression on the MDMs was also downregulated. The CCR5 gene knock-out was confirmed on the genomic level as well. The TALEN-treated MDMS showed increased resistance to HIV-1 infection compared with the un-edited controls after HIV-1 challenge. The result of this study provides evidence and support for using TALEN to knock out CCR5 as a method for curing HIV-1 infection.Open Acces