UP marine, computer scientists invent semi-automated fish monitoring device

UP marine, computer scientists invent semi-automated fish monitoring device

Published: June 23, 2023

By: Timothy James M. Dimacali

A diver carefully installs a stereo camera for FishDrop, a semi-automated fish census technology developed by UP scientists. (Photo credit: Prospero Naval, Jr., and Laura T. David)

Monitoring the health of marine environments is a laborious activity, but is essential for evaluating the success of reef protection and rehabilitation initiatives. A fish census commonly involves divers swimming along a transect line, usually marked by a plastic cord, and visually counting and identifying the fish species that they encounter. This painstaking process requires trained experts and highly knowledgeable divers to accurately record data on species, size, and abundance.

 

In 2016, Dr. Laura David of the University of the Philippines – Diliman College of Science Marine Science Institute (UPD-CS MSI), together with co-author machine intelligence expert Prof. Prospero C. Naval, Jr. of the UP Department of Computer Science (UPD-DCS) presented a conference paper entitled, “FishDrop: Estimation of Reef Fish Population Density and Biomass using Stereo Cameras” which proposed a semi-automated method that combines a stereo camera rig and image recognition software to allow for more efficient and accurate reef fish census. 

 

The proposed technology would enable divers with minimal training to obtain high-quality population and species distribution measurements using the specially developed stereo camera rig and fish video analyzer software.

 

FishDrop promises to help improve the Philippines’ reef resilience and biodiversity restoration efforts, and contribute towards the overall health of the country’s reef ecosystems.

A sample of what FishDrop sees and how it recognizes and logs fish during a census. (Photo credit: Prospero Naval, Jr., and Laura T. David)

This coming Monday, June 26, Dr. David is set to take the iStories stage to expound on ‘FishDrop’ and share their team’s journey not just in developing the technology, but also in successfully translating this groundbreaking innovation into a patent. 


“Perseverance is necessary to get the concept and the product translated into a patent and commercial venture. It has not been an easy road,” says Dr. David. Like any other intellectual property and patent applications, the journey for FishDrop has been tedious, nevertheless rewarding. Dr. David hopes that through her sharing, she may inspire others to persevere with their own scientific endeavors despite the trudging process.


iStories is a series of innovation-themed talks, storytelling, and activities featuring local and international scientists. The initiative aims to ignite the creativity and inventiveness of young scientists not just from UPD-CS but from other institutes inside and outside UP.

Its fourth session is scheduled for June 26, 2023, 3:00 pm at the MSI Audio Visual Room and will also be live via Zoom. To join, you may register through this link https://bit.ly/iStories3rd. 


The iStories series takes place at 3:00 pm on the last Monday of every month.  Subscription to individual sessions or the entire iStories webinar series is also possible through the same registration form. 


For inquiries about iStories, please message adride_staff@science.upd.edu.ph 


For interview requests and other media concerns, please contact media@science.upd.edu.ph 


Sources:

Naval, P. C., & David, L. T. (2016). FishDrop: Estimation of reef fish population density and biomass using stereo cameras. In 2016 Techno-Ocean (Techno-Ocean). DOI: 10.1109/Techno-Ocean.2016.7890710.

Agam-agam sa Agham: The current and future prospects of science communication in the Philippines

Agam-agam sa Agham: The current and future prospects of science communication in the Philippines

Published: June 21, 2023

By: Timothy James M. Dimacali

What can be done to improve weather and disaster reporting in the Philippines? How are scientists portrayed in Pinoy movies and pop culture? Where can we find the best examples of science communication for Filipino online viewers? When can we hope to develop a science-appreciative Filipino culture?

Explore the answers to these and other questions at “Agam-agam sa Agham: The current state and future prospects of science communication in the Philippines”. This free public lecture is a joint initiative of the UP Diliman College of Science (UPD-CS) and Science Communicators Philippines (SciCommPH). it will be held on June 30 (Friday), 2pm – 5pm at the UPD-CS Auditorium. It will also be streamed live to registered participants.

 

You can reserve a slot at the event and receive the Zoom login details by registering here: https://bit.ly/SciCommLectureReg

 

The list of distinguished speakers includes:

SciCommPH is a non-stock, non-profit national organization of scicomm practitioners and researchers, journalists, and scientists.

Pinoy appointed editor of esteemed int’l journal

Pinoy appointed editor of esteemed int’l journal

Published: June 21, 2023

By: Timothy James M. Dimacali

For the first time in its 77-year history, the esteemed scientific publication Optik: International Journal for Light and Electron Optics will be helmed by a Filipino scientist.

Prof. Percival F. Almoro of the University of the Philippines – Diliman College of Science National Institute of Physics (UPD-CS NIP) was appointed Section  Editor of the Optik journal by international scientific publishing house Elsevier as of June 2023. 

 

Established in 1946, Optik is an internationally-renowned scientific journal, having published in its pages works by famous physicists including R. W. Gerchberg and W. O. Saxton, for whom the phase retrieval algorithm is named. It is also the official journal of the German Society for Applied Optics, which counts among its honorary members Nobel Prize winners Stefan Hell (2014, super-resolved fluorescence microscopy) and Dennis Gabor (1979, holography).  As of 2021, Optik showcased an above-average impact factor of 2.84. 

 

In his new editorial capacity, Almoro will have final responsibility and the last word on the journal’s specialized content in areas ranging from optical metrology and interferometry to phase retrieval.

 

“This editorship stint  is a great honor not just for me but also for all Filipinos,” Almoro said. “It is a recognition on the international stage that researchers in the country can carry out good quality research.” 

 

For interview requests and other media concerns, please email media@science.upd.edu.ph.

From Sea to Sky: UPD-CS scientists feted for pioneering research

From Sea to Sky: UPD-CS scientists feted for pioneering research

Published: June 16, 2023

By: Timothy James M. Dimacali

From the deepest stretches of the ocean to the farthest reaches of the sky, Filipino scientists are adding to humanity’s collective knowledge of the world. Their efforts have not gone unsung, as recent explorations by University of the Philippines-Diliman College of Science (UPD-CS) researchers have earned acclaim from both national and international scientific and award-giving bodies.

The University of the Philippines - Diliman College of Science (UPD-CS) is one of the country’s premiere research and teaching institutions. In 2023, its outstanding researchers were honored locally and abroad by the NAST and Asian Scientist Magazine. (Photo credit: Nadine Lim, UP Photography Society)

The Philippine National Academy of Science and Technology-Philippines (NAST) recently recognized six members of the UPD-CS community: two were named Academician; two were recognized as outstanding young scientists (OYS); and two won the grand prize and a special citation in the 2023 NAST Talent Search for Young Scientists (NTSYS). Meanwhile an additional four UPD-CS researchers were highlighted in this year’s edition of the prestigious Asian Scientist 100.

New Academicians

 

The NAST is the Philippines’ highest scientific advisory and recognition body; its distinguished members are selected exclusively by the Academy itself and conferred the title, “Academician.” Gil S. Jacinto, PhD, of the UPD-CS Marine Science Institute (UPD-CS MSI) and Maria Corazon A. de Ungria, PhD, of the UPD-CS Natural Sciences Research Institute (UPD-CS NSRI), were recently inducted as Academicians for their respective work in marine chemistry and forensic DNA technology.

 

Jacinto’s research interests are in nutrient and trace elements in tropical marine environments, marine pollution chemistry, submarine groundwater discharge, hypoxia, and seawater carbonate chemistry. He was MSI director from 2000 to 2006 and established the Marine Chemistry and Pollution Laboratory at the MSI, the first chemical oceanography laboratory in the Philippines.

 

Meanwhile, De Ungria is known for her research in human population genetics and forensic DNA technology, which are invaluable tools for human identification in criminal investigation, disaster victim identification, and resolving parentage disputes. She provided technical assistance in drafting the Supreme Court Rule on DNA evidence, which was approved in 2007 and has since been used nationwide by the Philippine judicial system in handling sexual assault cases. She is the director of the Program on Biodiversity, Ethnicity, and Forensics at the Philippine Genome Center and concurrently heads the DNA Laboratory of the NSRI.

 

Outstanding Young Scientists

 

The NAST OYS award is given annually to Filipino scientists aged 41 and below who have made significant contributions to science and technology and have been published in reputable scientific journals.

 

Jillian Aira S. Gabo-Ratio, DEng, of the UPD-CS National Institute of Geological Sciences (UPD-CS NIGS), and Reinabelle C. Reyes, PhD, of the UPD-CS National Institute of Physics (UPD-CS NIP) were recognized as this year’s OYS in the field of earth resources engineering, and astrophysics, respectively.

 

Gabo-Ratio is an associate professor at NIGS, and is the institute’s officer-in-charge-deputy director for academic affairs. Her research interests are in economic geology, igneous and sedimentary geochemistry, geophysics, and tectonics. A topnotcher in the 2006 Geology Licensure Examination, Gabo-Ratio is a recipient of the UP Alumni of Michigan Centennial Professorial Chair (2021), One UP Faculty Grant (2019-2021), UPD Centennial Faculty Grant (2017-2021), and the UP System International Publication Award (2017-2022).

 

Reyes, an associate professor at the NIP, made worldwide headlines in 2010 with her paper, “Confirmation of General Relativity on Large Scales from Weak Lensing and Galaxy Velocities which confirmed Albert Einstein’s Theory,” which was published in the high-profile journal, Nature. In 2020, she established the NIP Data and Computation Research Group, which is focused on data-driven astrophysics and computational physics. 

 

NTSYS winners

 

Jayson Cosme, PhD, an associate professor at the NIP, is a theoretical physicist specializing in condensed matter. His paper, “Observation of a Continuous Time Crystal” clinched the grand prize at this year’s NTSYS. He also headed a recent study of dark matter, which resulted in a Nature Materials paper entitled, “Condensate Formation in a Dark State of a Driven Atom-Cavity System.” 

 

A special citation was also given to Charlon A. Ligson, MS in Marine Science from the MSI, for his paper, “Survival and sexual maturity of sexually propagated Acropora verweyi corals four years after outplantation.”

 

Asian Scientist 100

 

Meanwhile, Singapore’s Asian Scientist Magazine recently released the latest edition of its annual “Asian Scientist 100” list that fetes the region’s best and brightest researchers, touted as “Asia’s science superstars.” In the 2023 list are four scientists from UPD-CS: Pia D. Bagamasbad, PhD, from the UPD-CS National Institute for Molecular Biology and Biotechnology (UPD-CS NIMBB); Aletta T. Yñiguez, PhD, of the UPD-CS MSI;  and Allan Gil S. Fernando, PhD, and Mario Juan A. Aurelio, PhD, of UPD-CS NIGS.

 

Both Bagamasbad and Yñiguez were Philippine Outstanding Women in the Nation’s Service (TOWNS) awardees in 2022, for respectively spearheading an RT-PCR training program for the detection of SARS-CoV-2 in support of the country’s COVID-19 response, and for developing and advocating sustainable fishing practices among local communities. In the same year, Fernando was awarded the National Research Council of the Philippines’ Achievement Award in recognition of his contributions to earth and space science. For his part, Aurelio’s contributions to structural geology and geodynamics education earned him the 2022 Gregorio Y. Zara Award for Basic Research from the Philippine Association for the Advancement of Science and Technology (PhilAAST).

 

For interview requests and other concerns, please contact media@science.upd.edu.ph.

Pinoy scientist heads int’l study on dark quantum matter

Pinoy scientist heads int’l study on dark quantum matter

Published: May 30, 2023

By: Timothy James M. Dimacali

Filipino physicist Dr. Jayson Cosme from the University of the Philippines – Diliman College of Science National Institute of Physics (UPD-CS NIP) recently led a team of six Germany-based researchers in pioneering a way to make a special kind of “dark” matter that can’t be observed using standard laboratory methods. His team’s findings were published in the prestigious international journal, Physical Review Letters.

UPD-CS physicist Dr. Jayson Cosme led a team of German researchers in the creation of a dark-state Bose-Einstein condensate. Their groundbreaking work was published in Physical Review Letters. (Photo credit: Dr. Jayson Cosme)

Scientists are able to use laser beams to slow down the movement of the atoms in a material, causing its temperature to drop. When the temperature goes down almost to absolute zero, the individual atoms can condense together into a new state of matter with quantum properties that behaves almost like a single giant atom. Renowned physicists Albert Einstein and Satyendra Nath Bose were the first to predict its existence, hence it was named after them and is now called a Bose-Einstein Condensate (BEC).

 

BECs can be observed and studied using special cameras. However, Dr. Cosme’s team was able to use lasers to further manipulate them so that they can’t be observed using these standard methods. “By shaking BECs in the right way, we can cause them to become quantum objects that don’t absorb, reflect, nor emit light—hence, ‘dark,’” he explained.

The flame-like glow in this experimental setup is from Rubidium-87 atoms that are about to form a Bose-Einstein condensate. (Photo credit: Dr. Andreas Hemmerich)

Dr. Cosme expressed pride and gratitude at being given the opportunity to helm an international team composed of some of the foremost researchers in his field. “I’m very honored and thankful to have been the last author on this paper, as my colleagues are all working from Germany,” he said.

 

“This has been a very deep cooperation between myself and the group of Prof. Andreas Hemmerich, who studied under Nobel Laureate Theodor W. Haensch; as well as Prof. Ludwig Mathey’s group, which includes my close collaborator, first author Jim Skulte,” he explained.

 

For interview requests and other concerns, please contact media@science.upd.edu.ph.

 

Sources:

Jim Skulte, Phatthamon Kongkhambut, Sahana Rao, Ludwig Mathey, Hans Keßler, Andreas Hemmerich, and Jayson G. Cosme. Condensate Formation in a Dark State of a Driven Atom-Cavity System. Physical Review Letters. (2023). https://doi.org/10.1103/PhysRevLett.130.163603

UPD-CS scientist co-invents defense vs invasive alien species

UPD-CS scientist co-invents defense vs invasive alien species

Published: May 26, 2023

By: Eunice Jean C. Patron

Shipboard personnel oversee a live demonstration of the ballast water treatment system co-developed by UPD-CS IESM scientist Dr. Benjamin Vallejo Jr. The system is just a fraction of the cost of other commercially available solutions. (Photo credit: Dr. Benjamin Vallejo, Jr.)

All over the world, cargo ships and other large vessels routinely fill their ballast tanks with seawater to help keep afloat on rough seas. This ballast water is usually released at the ship’s destination, bringing with it invasive animals, plants, microorganisms and other alien species that can devastate local marine biodiversity and coastal ecosystems.

 

Such invasive alien species have cost over US$1.1 trillion worth of damage worldwide between 1960 and 2022 alone, according to an international study. The cost of managing invasions has cost the world an estimated US$95.3 billion since 1960.

 

This global problem prompted scientists from the University of the Philippines – Diliman College of Science (UPD-CS) and the University of Cebu to invent a port water treatment system that costs just ₱12 million or only around $200,000—a small fraction of the cost of other commercially-available systems, which can run as high as US$5 million.

 

“Our system utilizes UV sterilization and mechanical methods to treat ballast water, and has proven promising in initial tests in decreasing the number of invasive species translocated from port to port,”  said the system’s co-inventor, UPD-CS Institute of Environmental Science and Meteorology (IESM) Professor and Ballast Water and Biofouling Management Research Program Leader Dr. Benjamin Vallejo Jr. 

“It complies with the IMO D-2 standard for ballast water treatment and can be used until the local industry can install its own onboard treatment systems,” he added.

 

This is a very timely invention considering that, in 2018, the Philippines ratified the IMO’s 2004 Ballast Water Management Convention, which imposes regulations on the proper handling and treatment of ballast water. Thus, Philippine ships constructed after 2018 are mandated to have a port ballast water treatment system. And by 2024, all ships are expected to treat their ballast water before release.

A closeup of the ballast water treatment system co-invented by UPD-CS IESM scientist Dr. Benjamin Vallejo Jr. (Photo credit: Dr. Benjamin Vallejo)

“We hope this treatment system will be cheaper than other costly comparable systems. Now is the opportunity for Filipino investors to break into Southeast Asia’s ballast water treatment market,” Dr. Vallejo urged. 


Dr. Vallejo will discuss his alternative ballast water treatment system for ships at the upcoming iStories webinar hosted by UPD-CS on May 29, 2023. The webinar will dive deeper into the ideation process and development of the treatment system and its mass production and distribution.


iStories is a series of innovation-themed talks, storytelling, and activities featuring local and international scientists. The initiative aims to ignite the creativity and inventiveness of young scientists not just from UPD-CS but from other institutes inside and outside UP.

A computer-generated mockup of the ballast water treatment system co-invented by UPD-CS IESM scientist Dr. Benjamin Vallejo Jr.(Photo credit: Dr. Benjamin Vallejo)

The third session of iStories on May 29, 2023 (Monday) will be held on Zoom.

The iStories series is scheduled for 3:00 pm every last Monday of the month. To join, you may register through this link https://bit.ly/iStories3rd. Subscription to the entire iStories webinar series is also possible through the same form.

 

For inquiries about iStories, please message adride_staff@science.upd.edu.ph

 

For interview requests and other media concerns, please contact media@science.upd.edu.ph

 

Sources:

Ross N. Cuthbert et al. Biological invasion costs reveal insufficient proactive management worldwide. Science of The Total Environment, Volume 819, 2022. https://doi.org/10.1016/j.scitotenv.2022.153404 

Ballast Water Management. International Maritime Organization. (n.d.). https://www.imo.org/en/ourwork/environment/pages/ballastwatermanagement.aspx