TagLab

Last updated
TagLab
Developer(s) ISTI - CNR
Stable release
2023.5.17 / May 17, 2023;7 months ago (2023-05-17) [1]
Written in python
Operating system Cross-platform
Type Graphics software
License GPL
Website taglab.isti.cnr.it

TagLab is an interactive open source software system for facilitating the precise annotation of benthic species in orthophoto of the bottom of the sea. TagLab can automatically extract statistical informations about the evolution of monitored species and it segments large images using CNN-based algorithms. [2]

TagLab used also for the monitoring of the health of coral reefs, in order to quantify over large orthophotos of the seabed the extent of coral bleaching events. [3] Notable users of TagLab are MOTE Marine Laboratory, [4] the Hawaiʻi Institute of Marine Biology, [5] National Oceanic and Atmospheric Administration, [6] and Scripps Institution of Oceanography. [7]

TagLab is listed as one of the main tools for the standard operating procedures for the use of large-area imaging in tropical shallow water coral reef monitoring, research, and restoration. [8]

TagLab has won the 2023 VRVis Visual Computing Award for being "an open-source software solution that mitigates technological disparities between labs and promotes shared data standards and protocols". [9]

Related Research Articles

<span class="mw-page-title-main">Marine biology</span> Scientific study of organisms that live in the ocean

Marine biology is the scientific study of the biology of marine life, organisms in the sea. Given that in biology many phyla, families and genera have some species that live in the sea and others that live on land, marine biology classifies species based on the environment rather than on taxonomy.

<span class="mw-page-title-main">Coral</span> Marine invertebrates of the class Anthozoa

Corals are colonial marine invertebrates within the class Anthozoa of the phylum Cnidaria. They typically form compact colonies of many identical individual polyps. Coral species include the important reef builders that inhabit tropical oceans and secrete calcium carbonate to form a hard skeleton.

<span class="mw-page-title-main">Coral reef</span> Outcrop of rock in the sea formed by the growth and deposit of stony coral skeletons

A coral reef is an underwater ecosystem characterized by reef-building corals. Reefs are formed of colonies of coral polyps held together by calcium carbonate. Most coral reefs are built from stony corals, whose polyps cluster in groups.

<span class="mw-page-title-main">Coral bleaching</span> Phenomenon where coral expel algae tissue

Coral bleaching is the process when corals become white due to various stressors, such as changes in temperature, light, or nutrients. Bleaching occurs when coral polyps expel the zooxanthellae that live inside their tissue, causing the coral to turn white. The zooxanthellae are photosynthetic, and as the water temperature rises, they begin to produce reactive oxygen species. This is toxic to the coral, so the coral expels the zooxanthellae. Since the zooxanthellae produce the majority of coral colouration, the coral tissue becomes transparent, revealing the coral skeleton made of calcium carbonate. Most bleached corals appear bright white, but some are blue, yellow, or pink due to pigment proteins in the coral.

<span class="mw-page-title-main">Mote Marine Laboratory</span> Non-profit organisation in the USA

Mote Marine Laboratory is an independent, nonprofit, marine research organization based on City Island in Sarasota, Florida, with additional campuses in eastern Sarasota County, Boca Grande, Florida, and the Florida Keys. Founded in 1955 by Eugenie Clark in Placida, Florida, it was known as the Cape Haze Marine Laboratory until 1967. The laboratory aims to advance marine science and education, supporting conservation and sustainable use of marine resources. A public aquarium and associated education program interpret its research for the public.

<span class="mw-page-title-main">Fungiidae</span> Family of corals

The Fungiidae are a family of Cnidaria, commonly known as mushroom corals or plate corals. The family contains thirteen extant genera. They range from solitary corals to colonial species. Some genera such as Cycloseris and Fungia are solitary organisms, Polyphyllia consists of a single organism with multiple mouths, and Ctenactis and Herpolitha might be considered as solitary organisms with multiple mouths or a colony of individuals, each with its separate mouth.

<span class="mw-page-title-main">Giant barrel sponge</span> Species of sponge

The giant barrel sponge is the largest species of sponge found growing on Caribbean coral reefs. It is common at depths greater than 10 metres (33 ft) down to 120 metres (390 ft) and can reach a diameter of 1.8 metres. It is typically brownish-red to brownish-gray in color, with a hard or stony texture. The giant barrel sponge has been called the "redwood of the reef" because of its size and estimated lifespan of hundreds to a thousand or more years. It is perhaps the best-studied species of sponge in the sea; a population on Conch Reef, in the Florida Keys, has been monitored and studied since 1997.

<span class="mw-page-title-main">Watamu Marine National Park</span> Marine park in Kenya

Watamu Marine National Park and Reserve is located in Kenya. Established in 1968, it was one of Kenya's first marine parks. It is located about 90 miles (140 km) north of Mombasa, Kenya's second largest city. Its coral gardens are 300 metres (980 ft) from the shore and are home to approximately 600 species of fish, 110 species of stony coral and countless invertebrates, crustaceans and molluscs. Water temperature varies from 20 degrees Celsius to 30 degrees Celsius. The park was designated as a biosphere reserve in 1979.

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Sean Anderson is an American conservation biologist, restoration ecologist and professor of Environmental Science and Resource Management (ESRM) at California State University Channel Islands (CSUCI). He was educated at the University of California Santa Barbara, University of California Los Angeles and Stanford University. Anderson embraces education and research alike, managing projects from California to Oceania and the Middle East. His lab, named "PIRatE Lab", conducts a wide range of coastal monitoring, ecological restoration, and conservation efforts.

<span class="mw-page-title-main">Ocean acidification in the Great Barrier Reef</span> Threat to the reef which reduces the viability and strength of reef-building corals

Ocean acidification threatens the Great Barrier Reef by reducing the viability and strength of coral reefs. The Great Barrier Reef, considered one of the seven natural wonders of the world and a biodiversity hotspot, is located in Australia. Similar to other coral reefs, it is experiencing degradation due to ocean acidification. Ocean acidification results from a rise in atmospheric carbon dioxide, which is taken up by the ocean. This process can increase sea surface temperature, decrease aragonite, and lower the pH of the ocean. The more humanity consumes fossil fuels, the more the ocean absorbs released CO₂, furthering ocean acidification.

<span class="mw-page-title-main">Ruth Gates</span> American marine biologist (1962–2018)

Ruth Deborah Gates was the Director of the Hawaiʻi Institute of Marine Biology and the first woman to be President of the International Society for Reef Studies. Her research was dedicated to understanding coral reef ecosystems, specifically coral-algal symbiosis and the capacity for corals to acclimatize under future climate change conditions. Doctor Gates is most accredited with looking at coral biology and human-assisted coral evolution, known as super corals, as notably seen in the documentary Chasing Coral, available on Netflix.

<span class="mw-page-title-main">Coral Reef Conservation Program</span>

Coral Reef Conservation Program (CRCP) is a partnership between National Oceanic and Atmospheric Administration (NOAA) agencies, established in 2000. The program is a multidisciplinary approach, initiated by the NOAA, to managing and understanding coral reef ecosystems through research and the publication of data to support relevant partners involved in coral reef restoration.

<span class="mw-page-title-main">Environmental impact of recreational diving</span> Effects of scuba diving on the underwater environment

The environmental impact of recreational diving is the effects of recreational scuba diving on the underwater environment, which is largely the effects of diving tourism on the marine environment. It is not uncommon for highly trafficked dive destinations to have more adverse effects with visible signs of diving's negative impacts due in large part to divers who have not been trained to sufficient competence in the skills required for the local environment, an inadequate pre-dive orientation, or lack of a basic understanding of biodiversity and the delicate balance of aquatic ecosystems. There may also be indirect positive effects as the environment is recognised by the local communities to be worth more in good condition than degraded by inappropriate use, and conservation efforts get support from dive communities who promote environmental awareness, and teach low impact diving and the importance of respecting marine life. There are also global coral reef monitoring networks in place which include local volunteer divers assisting in the collection of data for scientific monitoring of coral reef systems, which may eventually have a net positive impact on the environment.

Kristen Marhaver is a marine biologist studying coral reefs and specializing in coral ecology, reproduction, and conservation. Marhaver is a senior scientist at CARMABI Marine Research Station. Marhaver was part of the group of scientists that successfully used frozen Elkhorn coral sperm to fertilize live coral eggs to raise the first lab-reared juveniles in nurseries. Some of the sperm and eggs were from geographically isolated corals of the same species. Their success allows for the possibility of breeding corals to be more resistant to increasing ocean water temperatures by breeding corals that already survive at warmer temperatures with those that live at colder temperatures.

<span class="mw-page-title-main">Electrified reef</span> Human-created underwater structure

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<span class="mw-page-title-main">Coral reef restoration</span> Restoration of coral reefs

Coral reef restoration strategies use natural and anthropogenic processes to restore damaged coral reefs. Reefs suffer damage from a number of natural and man-made causes, and efforts are being made to rectify the damage and restore the reefs. This involves the fragmentation of mature corals, the placing of the living fragments on lines or frames, the nurturing of the fragments as they recover and grow, and the transplantation of the pieces into their final positions on the reef when they are large enough.

<span class="mw-page-title-main">Piti Bomb Holes Marine Preserve</span>

Piti Bomb Holes Marine Preserve is a marine protected area comprising all of Piti Bay on the western coast of Guam, located off of the village of Piti in the Philippine Sea. The defining "bomb hole" features, named because they look like bomb craters in the reef flat, are actually natural percolation pits where fresh water filters into the shallow lagoon at a depth of 25 to 30 feet. The largest pit houses the commercial Fish Eye Marine Park tourist attraction, which includes a wooden pier to a underwater observatory and a Seawalker tour of the lagoon bottom. It is visited by more than 200,000 people annually. The Piti preserve is the most ecologically diverse of Guam's five marine preserves. The pit around Fish Eye is a popular snorkeling and recreational diving site.

<span class="mw-page-title-main">Coral reefs of Kiribati</span> Pacific Ocean Island chain

The Coral reefs of Kiribati consists of 32 atolls and one raised coral island, Banaba, which is an isolated island between Nauru and the Gilbert Islands. The islands of Kiribati are dispersed over 3.5 million km2 (1.4 million sq mi) of the Pacific Ocean and straddle the equator and the 180th meridian, extending into the eastern and western hemispheres, as well as the northern and southern hemispheres. 21 of the 33 islands are inhabited. The groups of islands of Kiribati are:

References

  1. "TagLab 17 release notes". Official GitHub repository. 2023-02-24.
  2. Pavoni, Gaia; Corsini, Massimiliano; Ponchio, Federico; Muntoni, Alessandro; Edwards, Clinton; Pedersen, Nicole; Sandin, Stuart; Cignoni, Paolo (2022). "TagLab: AI-assisted annotation for the fast and accurate semantic segmentation of coral reef orthoimages". Journal of Field Robotics. 39 (3): 246–262. doi:10.1002/rob.22049. S2CID   244648241.
  3. Kopecky, Kai L.; Pavoni, Gaia; Nocerino, Erica; Brooks, Andrew J.; Corsini, Massimiliano; Menna, Fabio; Gallagher, Jordan P.; Capra, Alessandro; Castagnetti, Cristina; Rossi, Paolo; Gruen, Armin; Neyer, Fabian; Muntoni, Alessandro; Ponchio, Federico; Cignoni, Paolo (18 August 2023). "Quantifying the Loss of Coral from a Bleaching Event Using Underwater Photogrammetry and AI-Assisted Image Segmentation". Remote Sensing. 15 (16): 4077. Bibcode:2023RemS...15.4077K. doi: 10.3390/rs15164077 . hdl: 11380/1316375 . ISSN   2072-4292.
  4. Combs, Ian. "MOTE - Coral Reef Ecosystems Program".
  5. "Hybrid Reef Coastal Erosion Project". 31 October 2016.
  6. Costa, Bryan; Sweeney, Edward; Mendez, Arnold (October 2022). "Leveraging Artificial Intelligence to Annotate Marine Benthic Species and Habitats". Noaa Technical Memorandum Nos Nccos. 306. doi:10.25923/7kgv-ba52.
  7. Riegl, Bernhard, ed. (2020). Population Dynamics of the Reef Crisis. Elsevier Science. pp. 174–177. ISBN   9780128215302.
  8. Sophie, Cook; G., Rojano, Sarah; B., Edwards, Clinton; A., Bollinger, Michael; Jordan, Pierce; Shay, Viehman, T. (2023). "Standard operating procedures for the use of large-area imaging in tropical shallow water coral reef monitoring, research and restoration: Applications for Mission: Iconic Reefs restoration in the Florida Keys National Marine Sanctuary". doi:10.25923/w8h9-4z75.{{cite journal}}: Cite journal requires |journal= (help)CS1 maint: multiple names: authors list (link)
  9. "Gaia Pavoni and Thomas Höllt win VRVis Visual Computing Award".