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Towards an accurate evaluation of deduplicated storage systems

Paulo, João; Reis, Pedro; Pereira, José Orlando; Sousa, António Luís
Fonte: CRL Publishing; CRL Publishing Publicador: CRL Publishing; CRL Publishing
Tipo: Artigo de Revista Científica
Publicado em /11/2013 Português
Relevância na Pesquisa
37.43131%
Deduplication has proven to be a valuable technique for eliminating duplicate data in backup and archival systems and is now being applied to new storage environments with distinct requirements and performance trade-offs. Namely, deduplication system are now targeting large-scale cloud computing storage infrastructures holding unprecedented data volumes with a significant share of duplicate content. It is however hard to assess the usefulness of deduplication in particular settings and what techniques provide the best results. In fact, existing disk I/O benchmarks follow simplistic approaches for generating data content leading to unrealistic amounts of duplicates that do not evaluate deduplication systems accurately. Moreover, deduplication systems are now targeting heterogeneous storage environments, with specific duplication ratios, that benchmarks must also simulate. We address these issues with DEDISbench, a novel micro-benchmark for evaluating disk I/O performance of block based deduplication systems. As the main contribution, DEDISbench generates content by following realistic duplicate content distributions extracted from real datasets. Then, as a second contribution, we analyze and extract the duplicates found on three real storage systems...

rpoS Mutants in Archival Cultures of Salmonella enterica Serovar Typhimurium

Sutton, Amy; Buencamino, Raphael; Eisenstark, Abraham
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /08/2000 Português
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27.463252%
Long-term survival under limited growth conditions presents bacterial populations with unique environmental challenges. The existence of Salmonella enterica serovar Typhimurium cultures undisturbed in sealed nutrient agar stab vials for 34 to 45 years offered a unique opportunity to examine genetic variability under natural conditions. We have initiated a study of genetic changes in these archival cultures. We chose to start with examination of the rpoS gene since, among gram-negative bacteria, many genes needed for survival are regulated by RpoS, the stationary-phase sigma factor. In each of 27 vials examined, cells had the rpoS start codon UUG instead of the expected AUG of Salmonella and Escherichia coli strains recorded in GenBank. Ten of the 27 had additional mutations in the rpoS gene compared with the X77752 wild-type strain currently recorded in GenBank. The rpoS mutations in the 10 strains included two deletions as well as point mutations that altered amino acid sequences substantially. Since these stored strains were derived from ancestral cells inoculated decades ago and remained undisturbed, it is assumed that the 10 rpoS mutations occurred during storage. Since the remaining 17 sequences were wild type (other than in the start codon)...

Surveillance of Childhood Influenza Virus Infection: What Is the Best Diagnostic Method To Use for Archival Samples?

Frisbie, Brent; Tang, Yi-Wei; Griffin, Marie; Poehling, Katherine; Wright, Peter F.; Holland, Kathy; Edwards, Kathryn M.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /03/2004 Português
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Despite the clinical importance of influenza virus in pediatric respiratory infections, the optimal set of diagnostic tests to use when conducting studies using archival samples is not clear. In this study, we compared diagnostic tests for influenza virus in 75 children younger than 5 years of age who presented with symptomatic respiratory infection during one of four influenza seasons, had negative viral cultures for other respiratory pathogens, and had both an archival nasal aspirate obtained at the time of illness and serology spanning that influenza season. For all eligible children, we compared the results of viral culture performed at the time of collection with serology and PCR of archival nasal aspirates. Using real-time viral culture as the “gold standard,” the test characteristics of PCR of archival nasal aspirates (sensitivity, 82%; specificity, 100%) and serology (sensitivity, 82%; specificity, 87%) were similar. The relatively low sensitivity of PCR of archival nasal samples in this study compared to that of PCR of fresh samples in a previous study suggests that RNA degradation occurred despite storage of the specimens at −70°C. RNA degradation would also explain why only 11 (52%) of 21 archival nasal samples that had positive influenza virus cultures at the time of collection had positive repeat cultures in the summer of 2000. Thus...

Processing of long-stored archival cervical smears for human papillomavirus detection by the polymerase chain reaction.

de Roda Husman, A. M.; Snijders, P. J.; Stel, H. V.; van den Brule, A. J.; Meijer, C. J.; Walboomers, J. M.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /08/1995 Português
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27.78806%
The efficiency of a freeze-thaw method, a proteinase K/Tween 20 lysis method and a guanidinium isothiocyanate/silica beads method for DNA extraction from fixed and Papanicolaou-stained cells from the cervical cancer cell line Siha was measured by beta-globin polymerase chain reaction (PCR). The GTC/silica beads method, which appeared superior, revealed a human papillomavirus (HPV) general primer-mediated PCR sensitivity of 50-500 copies of HPV 16 per sample using dilutions of fixed and stained Siha cells. Application to archival cervical smears (n = 116) revealed that the yield and size of amplifiable DNA decreases with storage time. The longer the storage time, the more repetitions of the whole procedure, including the lysis step, were required to extract sufficient amplifiable DNA. In this way, an overall beta-globin PCR positivity for 98% of the smears was reached. Further analysis revealed that a maximum size of 200 bp could be amplified from smears stored for up to 9 years. The method was validated by demonstrating by PCR the same HPV types in archival smears and corresponding cervical biopsies of cervical cancer patients. In conclusion, the GTC/silica beads method appears suitable to process archival cervical smears for HPV detection by PCR. provided that stepwise adjustments are made until beta-globin PCR positivity is obtained and primers are chosen which amplify a maximum of about 200 bp.

Utilization of Clinical Laboratory Information System Databases for Medical Education and Research

Boyd, James C.; Ladenson, Jack H.; Lewis, John W.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 17/10/1979 Português
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27.664324%
The clinical laboratory information system (CLIS) represents a potential medical resource whose value outside of its service role in laboratory data management has remained largely unexplored. We wrote several programs for performing on-line CLIS database searches and for archival storage and retrieval of data from CLIS databases. These applications showed that CLIS databases can be tapped to yield a potential wealth of information for medical education and research. Our experience also pointed out some problems: (1) CLIS database query languages were lacking. This necessitated local software development to perform on-line database searches. (2) In the absence of CLIS data archival systems for long-term data storage, we programmed our own and found it cumbersome to use. Future design efforts should be directed toward ease and flexibility of use. (3) Medical records coded discharge diagnoses retrieved from hospital discharge diagnosis archival files were frequently inaccurate as judged by patient chart review.

Factors Influencing the Degradation of Archival Formalin-Fixed Paraffin-Embedded Tissue Sections

Xie, Ran; Chung, Joon-Yong; Ylaya, Kris; Williams, Reginald L.; Guerrero, Natalie; Nakatsuka, Nathan; Badie, Cortessia; Hewitt, Stephen M.
Fonte: SAGE Publications Publicador: SAGE Publications
Tipo: Artigo de Revista Científica
Publicado em /04/2011 Português
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27.70689%
The loss of antigenicity in archival formalin-fixed paraffin-embedded (FFPE) tissue sections negatively affects both diagnostic histopathology and advanced molecular studies. The mechanisms underlying antigenicity loss in FFPE tissues remain unclear. The authors hypothesize that water is a crucial contributor to protein degradation and decrement of immunoreactivity in FFPE tissues. To test their hypothesis, they examined fixation time, processing time, and humidity of storage environment on protein integrity and antigenicity by immunohistochemistry, Western blotting, and protein extraction. This study revealed that inadequate tissue processing, resulting in retention of endogenous water in tissue sections, results in antigen degradation. Exposure to high humidity during storage results in significant protein degradation and reduced immunoreactivity, and the effects of storage humidity are temperature dependent. Slides stored under vacuum with desiccant do not protect against the effects of residual water from inadequate tissue processing. These results support that the presence of water, both endogenously and exogenously, plays a central role in antigenicity loss. Optimal tissue processing is essential. The parameters of optimal storage of unstained slides remain to be defined...

A hierarchical storage management (HSM) scheme for cost-effective on-line archival using lossy compression

Avrin, DE; Andriole, KP; Yin, L; Gould, RG; Arenson, RL
Fonte: Springer-Verlag Publicador: Springer-Verlag
Tipo: Artigo de Revista Científica
Publicado em /03/2001 Português
Relevância na Pesquisa
27.769763%
A hierarchical storage management (HSM) scheme for cost-effective on-line archival of image data using lossy compression is described. This HSM scheme also provides an off-site tape backup mechanism and disaster recovery. The full-resolution image data are viewed originally for primary diagnosis, then losslessly compressed and sent off site to a tape backup archive. In addition, the original data are wavelet lossy compressed (at approximately 25:1 for computed radiography, 10:1 for computed tomography, and 5:1 for magnetic resonance) and stored on a large RAID device for maximum cost-effective, on-line storage and immediate retrieval of images for review and comparison. This HSM scheme provides a solution to 4 problems in image archiving, namely cost-effective on-line storage, disaster recovery of data, off-site tape backup for the legal record, and maximum intermediate storage and retrieval through the use of on-site lossy compression.

Detection of MicroRNAs in Archival Cytology Urine Smears

Simonato, Francesca; Ventura, Laura; Sartori, Nicola; Cappellesso, Rocco; Fassan, Matteo; Busund, Lill-Tove; Fassina, Ambrogio
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 28/02/2013 Português
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27.500122%
MicroRNAs’ dysregulation and profiling have been demonstrated to be clinically relevant in urothelial carcinoma (UC). Urine cytology is commonly used as the mainstay non-invasive test for secondary prevention and follow-up of UC patients. Ancillary tools are needed to support cytopathologists in the diagnosis of low-grade UC. The feasibility and reliability of microRNAs profiling by qRT-PCR analysis (miR-145 and miR-205) in archival routine urine cytology smears (affected by fixation/staining [Papanicolau] and room temperature storage) was tested in a series of 15 non-neoplastic and 10 UC urine specimens. Only samples with >5,000 urothelial cells and with <50% of inflammatory cells/red blood cells clusters were considered. Overall, a satisfactory amount of total RNA was obtained from all the considered samples (mean 1.27±1.43 µg, range 0.06–4.60 µg). Twenty nanograms of total RNA have been calculated to be the minimal total RNA concentration for reliable and reproducible miRNAs expression profiling analysis of archival cytological smears (slope = -3.4084; R-squared = 0.99; efficiency = 1.94). miR-145 and miR-205 were significantly downregulated in UC samples in comparison to non-tumor controls. These findings demonstrate that urine archival cytology smears are suitable for obtaining high-quality RNA to be used in microRNAs expression profiling. Further studies should investigate if miRNAs profiling can be successfully translated into clinical practice as diagnostic or prognostic markers.

Isothermal Vitrification Methodology Development for Non-cryogenic Storage of Archival Human Sera

Less, Rebekah; Boylan, Kristin L.M.; Skubitz, Amy P.N.; Aksan, Alptekin
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Português
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27.849507%
Biorepositories worldwide collect human serum samples and store them for future research. Currently, hundreds of biorepositories across the world store human serum samples in refrigerators, freezers, or liquid nitrogen without following any specific cryopreservation protocol. This method of storage is both expensive and potentially detrimental to the biospecimens. To decrease both cost of storage and the freeze/thaw stresses, we explored the feasibility of storing archival human serum samples at non-cryogenic temperatures using isothermal vitrification. When biospecimens are vitrified, biochemical reactions can be stopped, the specimen ceases to degrade, and macromolecules can be stabilized without requiring cryogenic storage. In this study, 0.2, 0.4, or 0.8 M trehalose; 0, 0.005 or 0.01 M dextran; and 0 or 10% (v/v) glycerol was added to human serum samples. The samples were either dried diffusively as sessile droplets or desiccated under vacuum after they are adsorbed onto glass microfiber filters. The glass transition temperatures (Tg) of the desiccated samples were measured by temperature-ramp Fourier Transform Infrared (FTIR) spectroscopy. Sera samples vitrified at 4 ± 2 °C when 0.8 M trehalose and 0.01 M dextran were added and the samples were vacuum dried for two hours. Western immunoblotting showed that vitrified serum proteins were minimally degraded when stored for up to one month at 4 °C. About 80% of all proteins were recovered after storage at 4 °C on glass microfiber filters...

Protocols for dry DNA storage and shipment at room temperature

Ivanova, Natalia V; Kuzmina, Masha L
Fonte: John Wiley & Sons Ltd Publicador: John Wiley & Sons Ltd
Tipo: Artigo de Revista Científica
Português
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37.385903%
The globalization of DNA barcoding will require core analytical facilities to develop cost-effective, efficient protocols for the shipment and archival storage of DNA extracts and PCR products. We evaluated three dry-state DNA stabilization systems: commercial Biomatrica® DNAstable® plates, home-made trehalose and polyvinyl alcohol (PVA) plates on 96-well panels of insect DNA stored at 56 °C and at room temperature. Controls included unprotected samples that were stored dry at room temperature and at 56 °C, and diluted samples held at 4 °C and at −20 °C. PCR and selective sequencing were performed over a 4-year interval to test the condition of DNA extracts. Biomatrica® provided better protection of DNA at 56 °C and at room temperature than trehalose and PVA, especially for diluted samples. PVA was the second best protectant after Biomatrica® at room temperature, whereas trehalose was the second best protectant at 56 °C. In spite of lower PCR success, the DNA stored at −20 °C yielded longer sequence reads and stronger signal, indicating that temperature is a crucial factor for DNA quality which has to be considered especially for long-term storage. Although it is premature to advocate a transition to DNA storage at room temperature...

Towards an Open Source Archival Repository and Preservation System

Bradley, Kevin; Lei, Junran; Blackall, Chris
Fonte: Universidade Nacional da Austrália Publicador: Universidade Nacional da Austrália
Tipo: Working/Technical Paper; Working/Technical Paper
Português
Relevância na Pesquisa
57.87188%
This report identifies possible open source pathways for sustainable preservation and, more importantly, identifies the gaps in available technology and recommends a way for UNESCO to encourage digital communities to address that shortcoming. The report may be of some value to those intending to build a digital repository, but its intended audience are those who are responsible for, or are able to influence the direction of open source development so that a packagable and affordable sustainable digital archival storage system can be developed, supported and made available.; UNESCO; This project was sponsored jointly by UNESCO and the Australian Partnership for Sustainable Repositories, and carried out with the help of the National Library of Australia.

Towards an Open Source Archival Repository and Preservation System

Bradley, Kevin; Lei, Junran; Blackall, Chris
Fonte: Universidade Nacional da Austrália Publicador: Universidade Nacional da Austrália
Tipo: Working/Technical Paper; Working/Technical Paper
Português
Relevância na Pesquisa
57.87188%
This report identifies possible open source pathways for sustainable preservation and, more importantly, identifies the gaps in available technology and recommends a way for UNESCO to encourage digital communities to address that shortcoming. The report may be of some value to those intending to build a digital repository, but its intended audience are those who are responsible for, or are able to influence the direction of open source development so that a packagable and affordable sustainable digital archival storage system can be developed, supported and made available.; UNESCO; This project was sponsored jointly by UNESCO and the Australian Partnership for Sustainable Repositories, and carried out with the help of the National Library of Australia.

A survey and analysis of high density mass storage devices and systems

Schneidewind, Norman F.; Syms, Gordon H.; Grainger, Thomas L.; Carden, Robert J.
Fonte: Monterey, California. Naval Postgraduate School Publicador: Monterey, California. Naval Postgraduate School
Tipo: Relatório
Português
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A survey and analysis has been made of high density mass storage systems for the Navy Fleet Material Support Office. The purpose of the project was to survey mass storage devices and systems and to select several devices for detailed analysis. Representative devices were analyzed in order to determine their suitability for various file management functions. The major conclusions of the study are the following: 1. Mass storage devices have high potential for those applications which have a requirement to store a large data base (10ᄍ-10ᄍᄇ bits) on-line. 2. Mass storage devices should be considered as supplements to conventional storage devices for large data base applications, and used as part of a hierarchical storage system, rather than as replacements for conventional storage quipment. 3. Mass storage devices are not competitive with conventional storage equipment for direct access processing. 4. Erasable mass storage devices are competitive with conventional storage equipment for sequential file processing. 5. Non-erasable mass storage devices are inappropriate for high activity file processing but can be employed to advantage in archival storage applications. 6. As in the case of conventional storage units, the file activity ratio is a prime consideration in the selection of a file processing technique for mass storage. Low activity ratios favor address look-up or calculation and direct file access. High file activity ratios favor batched input and sequential file

Distributed exact deduplication for primary storage infrastructures

Paulo, João; Pereira, José Orlando
Fonte: Springer Publicador: Springer
Tipo: Conferência ou Objeto de Conferência
Publicado em //2014 Português
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37.43131%
Lecture Notes in Computer Science, Volume 8460, 2014; Deduplication of primary storage volumes in a cloud computing environment is increasingly desirable, as the resulting space savings contribute to the cost effectiveness of a large scale multi-tenant infrastructure. However, traditional archival and backup deduplication systems impose prohibitive overhead for latency-sensitive applications deployed at these infrastructures while, current primary deduplication systems rely on special cluster filesystems, centralized components, or restrictive workload assumptions. We present DEDIS, a fully-distributed and dependable system that performs exact and cluster-wide background deduplication of primary storage. DEDIS does not depend on data locality and works on top of any unsophisticated storage backend, centralized or distributed, that exports a basic shared block device interface. The evaluation of an open-source prototype shows that DEDIS scales out and adds negligible overhead even when deduplication and intensive storage I/O run simultaneously.

The Naval Postgraduate School secure archival storage system, Part I. Design

Schell, Roger R.; Cox, Lyle Ashton
Fonte: Monterey, California. Naval Postgraduate School Publicador: Monterey, California. Naval Postgraduate School
Tipo: Relatório Formato: 324 p. in various pagings : ill. ; 28 cm.
Português
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There is an increasing need tor systems which Drovide controlled access to multiple levels ot sensitive data and intormaticn. This rencrt comorises the first phase ot the realization ot such a system: the comprehensive design ot a multilevel secure tile storage system. This is the tocus ot an ongoing research oroject, which is currently in the early implementation phases. The design is based uocn security kernel technology as applied to modern multiple microcomputer arrays. This design is intended to interface with other (distributed) Drocessing elements, perhaps torminq the central hub ot a data secure network ot computers. The design would orovide archival shared storage while insuring that each interfacing processor accessed only that information appropriate. The design ohase of the orcject is presented in a series of three research reports (Masters Oegree theses) . These reports, reorinted in their entirety here are: (1) Capt, O'Conneli and Lt. Richardson's definition ot a secure multi-microprocessor family of operating systems; (2) Cant- Coleman's detailed security kernel design tor a member ot this family; and (3) Lt. Parks' hierarchical tile system designed to run under the control ot Capt. Coleman's security kernel.; supported in part by the Foundation Research Program of the Naval Postgraduate School with funds provided by the Chief of Naval Research; http://archive.org/details/navalpostgraduat00sche; Noool480WR00Q54

SEARS: Space Efficient And Reliable Storage System in the Cloud

Li, Ying; Guo, Katherine; Wang, Xin; Soljanin, Emina; Woo, Thomas
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 05/08/2015 Português
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27.514116%
Today's cloud storage services must offer storage reliability and fast data retrieval for large amount of data without sacrificing storage cost. We present SEARS, a cloud-based storage system which integrates erasure coding and data deduplication to support efficient and reliable data storage with fast user response time. With proper association of data to storage server clusters, SEARS provides flexible mixing of different configurations, suitable for real-time and archival applications. Our prototype implementation of SEARS over Amazon EC2 shows that it outperforms existing storage systems in storage efficiency and file retrieval time. For 3 MB files, SEARS delivers retrieval time of $2.5$ s compared to $7$ s with existing systems.; Comment: 4 pages, IEEE LCN 2015

RapidRAID: Pipelined Erasure Codes for Fast Data Archival in Distributed Storage Systems

Pamies-Juarez, Lluis; Datta, Anwitaman; Oggier, Frederique
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Português
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28.17839%
To achieve reliability in distributed storage systems, data has usually been replicated across different nodes. However the increasing volume of data to be stored has motivated the introduction of erasure codes, a storage efficient alternative to replication, particularly suited for archival in data centers, where old datasets (rarely accessed) can be erasure encoded, while replicas are maintained only for the latest data. Many recent works consider the design of new storage-centric erasure codes for improved repairability. In contrast, this paper addresses the migration from replication to encoding: traditionally erasure coding is an atomic operation in that a single node with the whole object encodes and uploads all the encoded pieces. Although large datasets can be concurrently archived by distributing individual object encodings among different nodes, the network and computing capacity of individual nodes constrain the archival process due to such atomicity. We propose a new pipelined coding strategy that distributes the network and computing load of single-object encodings among different nodes, which also speeds up multiple object archival. We further present RapidRAID codes, an explicit family of pipelined erasure codes which provides fast archival without compromising either data reliability or storage overheads. Finally...

The MDS Queue: Analysing the Latency Performance of Erasure Codes

Shah, Nihar B.; Lee, Kangwook; Ramchandran, Kannan
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Português
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27.465645%
In order to scale economically, data centers are increasingly evolving their data storage methods from the use of simple data replication to the use of more powerful erasure codes, which provide the same level of reliability as replication but at a significantly lower storage cost. In particular, it is well known that Maximum-Distance-Separable (MDS) codes, such as Reed-Solomon codes, provide the maximum storage efficiency. While the use of codes for providing improved reliability in archival storage systems, where the data is less frequently accessed (or so-called "cold data"), is well understood, the role of codes in the storage of more frequently accessed and active "hot data", where latency is the key metric, is less clear. In this paper, we study data storage systems based on MDS codes through the lens of queueing theory, and term this the "MDS queue." We analytically characterize the (average) latency performance of MDS queues, for which we present insightful scheduling policies that form upper and lower bounds to performance, and are observed to be quite tight. Extensive simulations are also provided and used to validate our theoretical analysis. We also employ the framework of the MDS queue to analyse different methods of performing so-called degraded reads (reading of partial data) in distributed data storage.

An Investigation into the development of an interactive archival catalog of art within the Rochester Institute of Technology

Clayman, Jill
Fonte: Rochester Instituto de Tecnologia Publicador: Rochester Instituto de Tecnologia
Tipo: Tese de Doutorado
Português
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RIT has no complete visual and /or factual catalog of the pieces of art presently displayed in public areas. Many pieces of work on campus are in desperate need of repair as well as plaques to identify the work. Visions, the only known bound record of a selection of artwork on the Henrietta campus, was produced by the RIT Communications Office in 1975. The Archives in Wallace Memorial Library have a small collection of slides of various artworks, however, many works of art are currently missing. Several valuable pieces of work were lost in the move from the city campus to Henrietta, and some pieces have yet to be removed from storage in Physical Plant. RIT is not fully aware of what is currently located in public areas. This interactive catalog will create a complete visual and factual catalog of the artwork located in public areas on the RIT Henrietta campus. Being interac tive, this catalog will include full-color images, sound, QuickTime movie clips and text about the piece of work, its location on campus, the artist, as well as any other relevant information that can be gathered on the work. The catalog will be user-friendly so that anyone with little or no computer experience will have no trouble operating the program. Information on the artwork along with a full-color image of the piece will be displayed on each card. This interactive archival catalog will be simple for anyone to use. People with or without computer skills or experience with multimedia applications should discover that this catalog is a faster and more entertaining way to retrieve data. This thesis will investigate past...

Mallory archival filmstrip registration

Morgan, Luke
Fonte: Rochester Instituto de Tecnologia Publicador: Rochester Instituto de Tecnologia
Tipo: Senior Project
Português
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This project will create a method for importing and registering archival filmstrips for analysis and digital storage. Images will be registered in the horizontal and vertical directions with subpixel accuracy, and a method for rotational registration will also be developed to compensate for camera movement. In addition, the three filmstrips used to develop the programs will be analyzed for possible sightings of climbers scaling Mount Everest in 1924.