Commercial depth cameras have recently been tested to work underwater with trade off in measured depth distance but providing several advantages over conventional depth acquisition sensors such as Sonars and LiDARS. The biggest advantage is real-time 3D reconstruction and significantly better accuracy for small scale 3D scanning of submerged objects. Since traditional issues that are faced while using normal imaging cameras such as dependence on light and turbidity of water etc. are avoided, commercial depth cameras can open a new direction in small scale 3D scene reconstruction. This paper is an extension of our previous work in which we provided proof of concept that the Microsoft Kinect v2, which is a time of flight depth sensor, provides real-time 3D scanning in underwater environment, albeit at a shorter distance. However, the working of the time of flight sensor showed several issues in depth measurement in underwater environment. Preliminary results after correction of the measured distance are also provided in this work. Furthermore, the RGB and NIR cameras of Kinect v2 are not designed to perform underwater. To cater for the unwanted effects in the depth values, camera calibration has been performed on underwater images acquired from Kinect v2 and the results are elaborated. A fast, accurate and intuitive refraction correction method has been developed providing real-time correction to the created 3D mesh.
Commercial time of flight depth camera such as the Kinect v2 have been shown to perform underwater for 3D scene reconstruction of underwater objects. However, to incorporate the additional noise and incorporating effect of refraction due to the change in the imaging medium, a customized user implementation of the underlying scene reconstruction algorithms with the additional developed filters needs to be developed. This paper presents the details and performance of such a graphical user interface developed for Kinect v2. The GUI is a customized implementation of the Kinect Fusion framework, and incorporates underwater camera calibration, noise filtering, time of flight correction and refraction correction filters developed to adapt Kinect Fusion for 3D scene reconstruction in an underwater environment. Details of the user interface and the effect of various sub-functions and additional correction filters on the performance of Kinect Fusion reconstruction are discussed in detail.
One of the major research directions in robotic vision focuses on calculating the real world size of objects in a scene using stereo imaging. This information can be used while decision making for robots, manipulator localization in the workspace, path planning and collision prevention, augmented reality, object classification in images and other areas that require object sizes as a feature. In this paper we present a novel approach to calculate real world object size using RGB-D image acquired from Microsoft Kinect™, as an alternative to stereo imaging based approaches. We introduce a dynamic resolution matrix that estimates the size of each pixel in an image in real world units. The main objective is to convert the size of
objects represented in the image in pixels; to real world units (such as feet, inches etc.).We verify our results using available OpenSource RGB-D datasets. The experimental results show that our approach provides accurate measurements.
This paper presents preliminary work to utilize a commercial time of flight depth camera for real-time 3D scene reconstruction of underwater objects. Typical RGB stereo camera imaging for 3D capturing suffers from blur and haziness due to turbidity of water in addition to critical dependence on light, either from natural or artificial sources. We propose a method for repurposing the low-cost Microsoft Kinect™ Time of Flight camera for underwater environment enabling dense depth data acquisition that can be processed in real time. Our motivation is the ease of use and low cost of the device for high quality real-time scene reconstruction as compared to multi view stereo cameras, albeit at a smaller range. Preliminary results of depth data acquisition and surface reconstruction in underwater environment are also presented. The novelty of our work is the utilization of the Kinect depth camera for real-time 3D mesh reconstruction and our main objective is to develop an economical and compact solution for underwater 3D mapping.
This paper presents preliminary results of using commercial time of flight depth camera for 3D scanning of underwater objects. Generating accurate and detailed 3D models of objects in underwater environment is a challenging task. This work presents experimental results of using Microsoft Kinect™ v2 depth camera for dense depth data acquisition underwater that gives reasonable 3D scanned data but with smaller scanning range. Motivations for this research are the user friendliness and low-cost of the device as compared to multi view stereo cameras or marine-hardened laser scanning solutions and equipment. Preliminary results of underwater point cloud generation and volumetric reconstruction are also presented. The novelty of this work is the utilization of the Kinect depth camera for real-time 3D mesh reconstruction and the main objective is to develop an economical and compact solution for underwater 3D scanning.


The Image to the left superimposes the Exxon Valdez oil spill on the east coast of the US. The BP Horizon oil spill in April 2010 was more than 15 times larger than the Exxon Valdez oil spill.
Our local Outer Banks economy will shoulder the risk of damages from drilling offshore while the financial benefits of drilling go to the oil companies who secure the leases. Royalties are also paid to the federal government from oil and gas revenues but are not distributed to the state or local economies. There are no rewards of any kind for local residents of coastal communities but it is the residents and local coastal communities that carry a full burden of the risks of offshore drilling.
The risks are significant and a spill would cost the Outer Banks hundreds of millions of dollars in tourism income, thousands of jobs, and damage fragile fisheries and fragile ecosystems. Damages would not only impact the Outer Banks but currents would likely carry oil and other pollutants upstream (Gulf Stream) and down stream (Labrador Current). It is common knowledge that gulf stream waters are in a dynamic interchange with beaches and estuaries.
The process of exploring for oil is damaging and the pollutants introduced from "non-toxic oilfield waste" is highly toxic and would have a devastating effect on one of the most biologically dense and bio-diverse areas of the world.
The powerful hurricanes that batter our coasts can destroy drilling platforms, underwater pipelines and coastal storage tanks, dumping millions of gallons of oil, as happened with Hurricane Katrina on Sept 1. As documented by SKY Truth the satellite imagery below show spills flowed unimpeded for several weeks after Hurricane Katrina. Similar activity in the Atlantic would add insult to injury by pouring oil on beaches in addition to the significant property damage that typically accompanies hurricanes.
It is common knowledge that very few local jobs are created through offshore drilling as workers are shipped in from other areas and support infrastructure would be flown in or serviced out of the Chesapeake Bay area.,
According to the US Department of energy, less than 5% of the remaining oil and gas in the world exists in the U.S.
26% of the world?s annual energy is consumed by the U.S. although we have only 5% of the population. More than 50% of the remaining oil and gas exists in deposits located in the Middle East. The US can not become energy independent by drilling for oil.
Oil Companies already have thousands of leases they are not developing. 80% of the nation?s undeveloped, economically recoverable Outer Continental Shelf (OCS) gas is located in the Central and Western Gulf of Mexico (Mineral Management Service 2004)
Bureau of Land Management (BLM) data indicates that the vast majority of federal lands currently under lease are not being developed. Drilling permit approvals on Western public lands by the BLM increased in 2004 to a record number of 6,052, while the number of new wells that were drilled declined by nearly 10 percent, to 2,702. There is no NEED to drill off North Carolina?s Coast. Oil and gas resources are available to the oil companies , but they are not developing the leases they have.
It is also understood that Oil Companies sell the resources in the most favorable markets which will not likely be the US markets.
We assert that drilling should not be considered off North Carolina. In 1990, after Congress passed the North Carolina Outer Banks Protection Act, prohibiting leasing and drilling on federal seabed offshore from North Carolina Mobile Oil abandoned their leases.
In the Outer Banks Protection Act Congress found in 1990 that: (1) the Outer Banks of North Carolina is an area of exceptional environmental fragility and beauty; (2) the annual economic benefits of commercial and recreational fishing activities to North Carolina, which could be adversely affected by oil or gas development offshore the State's coast, exceeds $1,000,000,000; (3) the major industry in coastal North Carolina is tourism, which is subject to potentially significant disruption by offshore oil or gas development;
Mobil was denied a permit to explore for oil or gas off the coast of North Carolina. We are also aware that Chevron abandoned their leases off North Carolina in 1998.
Drilling in Hurricane & Storm plagued waters, has proven to be disastrous.
North Carolina is being pressured to put its vibrant economy at risk when nothing is being done on a national scale to conserve resources.
We strongly oppose drilling in the waters off North Carolina or anywhere else off the east coast of the US.
Michael McOwen, Past President of LegaSea


Publications (1 result)
Agassiz, A. E., L. F. de Pourtales, and T. Lyman. 1878. Reports on the results of dredging, under the supervision of Alexander Agassiz, in the Gulf of Mexico, by the United States Coast Survey Steamer "Blake," Lieutenant-Commander C.D. Sigsbee, U.S.N., Commanding. II. Report on the Echini by Alexander Agassiz, Crinoids and Corals by L.F. de Pourtales, and Ophiurans, by Theodore Lyman. Bulletin of the Museum of Comparative Zoology 5(9):2–368.


More than 90 percent of the wild salmon in the east-sea region is produced in the Gulf of Bothnia, where several large rivers flow. This is also where the salmon begins their migration to the southern Baltic Sea, to grow larger. After a couple of years, most of the salmon return to their native rivers to spawn and reproduce.
Salmon have been fished along the coast of the Gulf of Bothnia since the Middle Ages and for centuries this has been a significant industry for the area. During the war years, large quantities of salmon were caught because fishing in the Baltic Sea was then non-existent.
Nowadays, the EU has restricted salmon fishing in the Gulf of Bothnia. This may only take place during certain times and is limited by an annual quota. The severe restrictions on sea fishing in the southern Baltic Sea have meant that the supply of salmon in the Gulf of Bothnia has increased significantly, which means that fishing is improving for the coastal fishermen. The large rivers have met the researchers’ requirements for migrating salmon and reproduction, which is why this part of the salmon fishery is conducted in a sustainable way.


Climate Change Cinema explores pairings of current, classic, and cult films with lively introductions and conversations by notable figures from the world of science and technology around the topics of climate change and sea level rise. As our community is situated between the Everglades and the Atlantic, we seek to illuminate and explore scientific issues related to our environment that have a tangible impact on our lives.
Aug 9 at Venture Cafe/CIC Miami
For our launch event, we’re presenting the South Florida premiere of SAVING ATLANTIS, a documentary about one of the most consequential issues of our time: the dramatic decline of global coral reef ecosystems and the impact on human populations that depend on them
A post-film roundtable discussion will be led by Stephanie Rosales, a research scientist with the University of Miami and the National Oceanic and Atmospheric Association and include a panel of distinguished scientist from UM Rosenstiel School of Marine & Atmospheric Science and Oregon State University.
*PLEASE NOTE – THIS EVENT IS HAPPENING AT THE VENTURE CAFÉ MIAMI (EVERGLADES ROOM at CIC Miami) @ 1951 NW 7th Ave. Miami, FL, 33136*
Following the screening Dr. Stephanie Rosales will lead a roundtable discussion with Dr. Van Hooidonk, Nikki Traylor-Kownles and Ryan McMinds about climate change and its affect on our coral reefs.


The Marine Institute “Station Biologique de Roscoff”, located on the Brittany coast of the English Channel, is a research and training center in marine biology and oceanography, founded in 1872 by the Paris VI University Pierre and Marie Curie (UPMC) that also belongs to the national research center (CNRS). Its missions are both to promote research and education on the biology of marine organisms and ecosystems and to provide access, to staff and non-resident researchers, to the ecological and biological resources of the site. As a sea-front laboratory equipped with marine facilities and an integrative biology platform with dedicated staff, the SBR provides a unique scientific and technical environment for researchers, who wish to apply modern approaches to the study of marine organisms, notably micro- and macroalgae, invertebrates, and fish.
Dr. Mirjam Czjzek.
Research Director, CNRS.
Education: She is crystallographer by education and has discovered the world of CAZymes by working on crystal structures of cellulases and beta-glucosidases for several years in the group of Bernard Henrissat in Marseille, France. She has twenty years of experience in structural biology focusing on the structure/function relationship of polysaccharide degrading enzymes. She has actively participated to 5th and 6th FP European research projects EUROCELL and EDEN that aimed at understanding the synergistic enzymatic degradation of cellulose and hemicelluloses. In this context, she was involved in the elucidation of one of the first cellulase crystal structures and the first SAXS structures of mini-cellulosomes.
Interests: In 2005 she moved to the Station Biologique de Roscoff (CNRS, Centre National de Recherche Scientifique), where her research program entitled ‘marine glycobiology’ currently focuses on the structures and functions of carbohydrate-active enzymes, including their CBMs, which are involved in marine algal cell wall polysaccharide depolymerization. Her group studies the identification and the characterization of enzymes involved in the degradation, modification and the biosynthesis of the cell wall polysaccharides of plant and marine macro-algae. One particular goal is to establish the molecular bases of the protein – polysaccharide interactions, combining biochemical approaches (expression and purification of recombinant polysaccharidases from heterologous systems, directed mutagenesis, enzymology, etc) with crystal structure methods, and to dissect the 3D architecture of full length enzymes and complexes by combining crystallography with SAXS.
Role in CellulosomePlus: Characterization the atomic and supramolecular structure of candidate components by X-ray diffraction and SAXS (leader of WP 4).


Associate Professor Emeritus of Biological Sciences
PhD, 1966 Univ. of California - Los Angeles
|Office:||5A Tucker Hall|
Symbiosis and gene expression in an experimental system.
Research descriptionI study the biology of marine bacteria. These bacteria are microbes of merit because they produce commercially important enzymes; they are the source of next generation antibiotics; they are successful symbionts of eukaryotic hosts. Colonization of artificial surfaces by marine bacteria is not “meritorious” because the damage caused to the hulls of ships, for example, is highly expensive to repair! Despite their economic and ecological importance the genomes of marine bacteria have not been extensively studied.
We utilized standard RNAseq to investigate metabolic activities of Pseudoalteromonas strains. We are continuing to annotate the genomes of these marine bacteria using homology and gene context methods.
Pseudoalteromonads were first isolated from nature as symbionts of plants and animals. Although the subject of intense investigation symbiotic relationships are generally studied in well-established systems. When suspensions of Pseudoalteromonas piscicida and Zebra fish fibroblast cells are mixed in tissue culture the bacteria are taken up. We are using this model system to sample the population and isolate mRNA before and at various times after first contact. Bioinformatics and functional genomics are used to identify changes in gene expression as the association develops.
Givan,S, Zhou,M-Y, Bromert,K, Bivens,N, Chapman, L.F. 2015. Genomes released to NCBI
1. Pseudoalteromonas flavipulchra. Accession number JTDZ00000000
2. Pseudoalteromonas distincta. Accession number JWIG00000000
3. Pseudoalteromonas elyakovii Accession number JWIH 00000000
4. Givan SA, Zhou M-Y, Bromert K, Bivens N, Chapman LF. 2015. Genome sequences of the Pseudoalteromonas strains ATCC BAA-314, ATCC 70018, and ATCC 70019．Genome Announc 3(3):e00390-15. doi:10.1128/genomeA.00390-15.