biomedical

��ӽ紫ý to host International Workshop on Biodesign Automation this June

Charles Ferrer — Wed, 08 Apr 2026 15:55:56 +0000

��ӽ紫ý to host International Workshop on Biodesign Automation this June Charles Ferrer Wed, 04/08/2026 - 09:55

Charles Ferrer

The University of Colorado Boulder will host the 18th annual International Workshop on Biodesign Automation (IWBDA) on June 18-20. IWBDA will be held immediately following the Synthetic Biology: Engineering, Evolution & Design (SEED) Conference, which will be held in Denver from June 15-18.

Graduate and undergraduate students at a synthetic biology outreach event led by the Genetic Logic Lab at ��ӽ紫ý.

“Hosting IWBDA is a great opportunity for our faculty and students to engage with world-class researchers and industry leaders in the emerging field of synthetic biology,” said Chris Myers, department chair of electrical, computer and energy engineering. “We look forward to forming new collaborations that will move this exciting field forward.”

Synthetic biology involves redesigning organisms for useful purposes by engineering them to have new abilities. Scientists around the world are harnessing synthetic biology to solve the pressing problems in medicine, manufacturing and agriculture.

For example, microorganisms can be engineered to clean pollutants from water, soil and air that are essential in the fight against environmental contamination. In agriculture, scientists have modified rice to produce beta-carotene, a nutrient typically associated with carrots, helping to prevent vitamin A deficiency in populations that rely heavily on rice as a dietary staple.

However, synthetic biology faces a significant challenge where the field has lagged behind other industries when it comes to adopting computational and digital solutions. Unlike software engineering, where standardized tools and workflows are common, biological systems are highly complex and variable. A solution that works for one organism or process often must be completely redesigned for another.

This is where biodesign automation (BDA) comes in. BDA applies the principles of engineering and computer science to streamline and accelerate biological research and development.

By developing innovative software tools, standardized components and automated workflows, researchers aim to make synthetic biology faster, more reproducible and accessible.

IWBDA pushes the mission forward bringing synthetic biology, systems biology and design automation communities together for stronger collaboration.

What to expect at the SEED conference

Synthetic Biology: Engineering, Evolution & Design (SEED) is the premier technical conference for the synthetic biology community, serving as a global venue to share transformative breakthroughs across academia and industry.

Attending SEED 2026

Who: Open to the public
When: Monday, June 15- Thursday, June 18
Where: Hyatt Regency Denver at Colorado Convention Center
Registration: Required

The conference highlights how advances such as artificial intelligence and biological engineering are accelerating the field faster than ever.

Covering synthetic biology from its scientific foundations to its commercial applications, SEED offers attendees insight into development strategies from leaders in research, biomanufacturing and product innovation.

Whether participants focus on research and development, commercialization or bringing discoveries into real-world impact, SEED provides significant networking opportunities for those engaged in the synthetic biology community.

By attending both SEED and IWBDA, participants gain an opportunity to engage in technical workshops, as well as hands-on design automation strategies for individuals in research, academic and industry.

Get the scoop about IWBDA 2026

IWBDA aims to bring academic researchers and industry partners together to lead the field of biodesign automation for synthetic biology forward.

Attending IWBDA 2026
Who: Researchers, faculty, students, industry
When: Thursday, June 18 to Saturday, June 20
Where: KOBL 352 / ECCS 201
Registration: Required

This year’s IWBDA workshop, led by the Department of Electrical, Computer & Energy Engineering (ECEE), takes place immediately following the SEED conference, held in Boulder which is less than 40 miles from Denver, making the two events a natural pairing for attendees traveling to Colorado for the week.

IWBDA will include presentations and poster talks selected from submitted abstracts, Birds of a Feather discussions and interactive breakout sessions.

Topics will span artificial intelligence and machine learning in synthetic biology, biosecurity considerations in lab automation, the growing role of biofoundries, computer-aided design tools and synthetic biology education and outreach.

Keynote speakers include Dr. Domitilla Del Vecchio of MIT and Dr. Emma J. Chory of Duke University, both prominent researchers in the intersection of engineering and biological sciences.

Hands-on tutorials

Attending IWBDA Tutorials

Who: Researchers, faculty, students, industry
When: Saturday, June 13 to Sunday, June 14
Where: KOBL 352
Registration: Required (fee can be waived for CU students)

For those who want to dive deeper before the main workshop, IWBDA tutorials will be held June 13-14 in Boulder.

These two days hands-on sessions are designed to give faculty, researchers, industry members and students practical experience with synthetic biology software tools and to close the gap between tool developers and experimental biologists.

Parallel tracks will be offered for both users and developers, allowing attendees to tailor their experience to their skill level and interests.

The user track will guide participants through a complete synthetic biology workflow using open-source tools, while the developer track will introduce libraries and resources for building standard-enabled synthetic biology software.

��ӽ紫ý will host the 18th International Workshop on Biodesign Automation (IWBDA), June 18–20, following the SEED Conference in Denver. The workshop brings together researchers and industry leaders advancing biodesign automation in synthetic biology.

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Researchers pioneer fluid-based laser scanning for brain imaging

Charles Ferrer — Tue, 14 Oct 2025 21:55:50 +0000

Researchers pioneer fluid-based laser scanning for brain imaging Charles Ferrer Tue, 10/14/2025 - 15:55

Charles Ferrer

Quiroz with the laser scanning microscope used for the optical scanning research project.

Darwin Quiroz is exploring new frontiers in miniature lasers with major biomedical applications.

When Quiroz first started working with optics as an undergraduate, he was developing atomic magnetometers. That experience sparked a growing curiosity about how light interacts with matter, an interest that has now led him to a new technique in optical imaging.

Quiroz, a physics PhD student in the lab of Professor Juliet Gopinath in the Department of Electrical, Computer and Energy Engineering, and also co-advised by Professor Victor Bright from Paul M. Rady in Mechanical Engineering, is co-first author of a new study that demonstrates how a fluid-based optical device known as an electrowetting prism can be used to steer lasers at high speeds for advanced imaging applications.

The work published in Optics Express, conducted along with mechanical engineering PhD graduate Eduardo Miscles and Mo Zohrabi, senior research associate, opens the door to new technologies in microscopy, LiDAR, optical communications and even brain imaging.

“Most laser scanners today use mechanical mirrors to steer beams of light,” Quiroz said. “Our approach replaces that with a transmissive, non-mechanical device that’s smaller, lower-power and potentially easier to scale down into miniature imaging systems.”

Traditional laser scanning microscopy works by directing a focused beam of light across a sample like a grid one line at a time. This method provides powerful, high-resolution images of cells and neurons, but it requires fast, precise steering of the laser beam.

That’s where the electrowetting prism comes in. Unlike solid mirrors, the prism uses a thin layer of fluid whose surface can be precisely controlled with voltage. By altering the liquid’s shape, researchers can bend and steer light beams without moving mechanical parts.

Previous work with electrowetting prisms was limited to slow scanning speeds or one-dimensional beam steering.

Quiroz and Miscles pushed the technology further, demonstrating two-dimensional scanning at speeds from 25-75 hz, a milestone toward making the devices practical for real-world imaging.

“A big challenge was learning how to drive the device in a way that produces linear, predictable scanning without distortion,” Quiroz said. “We discovered that the prism has resonant modes like standing waves that we could actually leverage for scanning at higher speeds.”

The promise of this technology extends far beyond the lab. Since electrowetting prisms are compact and energy efficient, they could be integrated into miniature microscopes small enough to sit on top of a mouse’s head.

“Imagine being able to watch brain activity in real-time while an animal runs through a maze,” said Quiroz. “That’s the kind of in-vivo imaging this technology could enable and it could transform how we study neurological conditions like PTSD or Alzheimer’s disease.”

The project builds on earlier work in the Gopinath and Bright labs, where former PhD student Omkar Supekar first integrated an electrowetting prism into a microscope system for one-dimensional scanning.

By extending the technique into two dimensions and higher speeds, Quiroz and Miscles established a framework for calibrating and characterizing electrowetting scanners for a wide range of applications.

Looking ahead, Quiroz hopes this research not only improves imaging systems but also inspires future collaborations across fields.

“This work shows what’s possible when you combine physics and engineering approaches,” Quiroz said. “The ultimate goal is to build tools that help us see and understand the brain in ways we couldn’t before.”

Researchers explored a fluid-based optical device known as an electrowetting prism to steer lasers at high speeds for advanced imaging applications. This new frontier in miniature lasers opens the door to new technologies in microscopy, LiDAR, optical communications and even brain imaging.

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New optical technique could transform brain imaging in animals

Charles Ferrer — Thu, 04 Sep 2025 14:10:32 +0000

New optical technique could transform brain imaging in animals Charles Ferrer Thu, 09/04/2025 - 08:10

Charles Ferrer

Catherine Saladrigas

��ӽ紫ý postdoc Catherine Saladrigas is helping bring high-resolution imaging into miniature microscopes for neuroscience research.

In a promising leap forward for imaging, Saladrigas and a team of researchers have developed an optical method that could one day allow scientists to observe brain activity in animals with more clarity, which could provide insights for the human brain. Their research, published in Applied Physics Letters, tackles one of the key challenges in brain imaging: how to miniaturize complex optical systems without sacrificing resolution or contrast.

Saladrigas has been exploring ways to translate benchtop imaging techniques into tiny, head-mounted microscopes working alongside Professors Juliet Gopinath in the Department of Electrical, Computer and Energy Engineering and the Department of Physics and Victor Bright in the Paul M. Rady Department of Mechanical Engineering. These devices could enable real-time, in vivo studies of neural activity in animals yielding payoffs in the areas of neuroscience.

“Our goal was to come up with a strategy for high-resolution, high-contrast imaging that would work well in a miniaturized system,” Saladrigas said.

Traditional pixel-shifting technologies like those used in digital projectors and cameras enhance image resolution by making tiny sub-pixel movements. But in imaging systems, achieving this effect typically requires bulky optics or mechanically stabilized components. Both would be difficult for compact systems like wearable microscopes.

To overcome these design limitations, the team turned to a lesser-used technology: the tunable electrowetting prism, an electrically tunable liquid prism. This optical component uses fluid dynamics and electric fields to adjust the angles of a prism and shift an image laterally without any mechanical parts.

“We showed that an electrowetting prism could perform the image-shifting normally done with much bulkier components,” Saladrigas said. “That makes it a great opportunity for miniature imaging systems.”

The inspiration came from an unlikely place: projector technology. Saladrigas adapted a technique called wobulation, originally developed to make digital projectors appear higher resolution.

In wobulation, a display flickers between slightly offset images to create the perception of finer detail. Her team applied a similar concept to structured illumination microscopy, an imaging method that enhances contrast by shining patterned light on a sample.

“No one has applied a wobulation-like method to structured light microscopy before,” Saladrigas said, “and certainly not with a tunable electrowetting device.”

Though the project is still in its early stages, initial results are encouraging. The team successfully demonstrated the method on a benchtop system using test patterns.

“We compared our experimental results to theoretical predictions and were really happy with how close the results were,” she said.

The project drew on expertise from across the university and beyond. Saladrigas credited Bright’s background in fabrication and electrowetting devices, Gopinath’s optics experience and the contributions of colleagues like Eduardo Miscles, a former PhD student in mechanical engineering, who fabricated the device. The team also collaborated with researchers from Columbia University, Vikrant Kumar and Professor John Kymissis, who developed the custom LED light source used in the project.

The next phase? Miniaturization. Saladrigas is setting sights to integrate the technique into an actual head-mounted microscope, ideally one that can be tested on freely moving mice or voles in collaboration with ��ӽ紫ý and CU Anschutz neuroscientists.

“There’s so much happening in the brain during behavior with motion and visual cues,” Saladrigas said, “and we want to give neuroscientists a clearer window into all of it.”

��ӽ紫ý postdoc Catherine Saladrigas is helping bring high-resolution imaging into miniature microscopes for neuroscience research.

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New bioimaging device holds potential for eye and heart condition detection

Charles Ferrer — Wed, 13 Aug 2025 16:21:08 +0000

New bioimaging device holds potential for eye and heart condition detection Charles Ferrer Wed, 08/13/2025 - 10:21

Charles Ferrer

If you’ve been to a routine eye exam at the optometrist’s office, chances are you’ve had to place your chin and forehead up close to a bioimaging device.

It’s known as optical coherence tomography (OCT) and widely used in eye clinics around the world. OCT uses light waves to take high-resolution, cross-sectional images of the retina in a non-invasive manner.

Samuel Gilinsky

These images can be essential for diagnosing and monitoring eye conditions.

In any bioimaging — either retinal or in-vivo, imaging that takes place inside the human body — devices require them to be quite small, compact that can produce high-quality images.

However, mechanical aspects of OCT devices, like spinning mirrors can increase the chance of device failure.

Researchers at ��ӽ紫ý have developed a new bioimaging device that can operate with significantly lower power and in an entirely non-mechanical way. It could one day improve detecting eye and even heart conditions.

In a recent study published in Optics Express, the team of engineers created a device that uses a process called electrowetting to change the surface shape of a liquid to perform optical functions.

“We are really excited about using one of our devices, in particular for retinal imaging,” said lead author Samuel Gilinsky, a recent PhD graduate in electrical engineering. “This could be a critical technique for in-vivo imaging for inside our bodies.”

By creating a device that doesn’t use scanning mirrors, the technique requires less electrical power than other devices used for OCT and bioimaging.

“The benefits of non-mechanical scanning is that you eliminate the need to physically move objects in your device, which reduces any sources of mechanical failure and increases the overall longevity of the device itself,” Gilinsky said.

Gilinsky noted the need for these OCT systems to be compact, lightweight and, most importantly, safe for use for the human body.

Other members of the research team included Juliet Gopinath, professor of electrical engineering; Shu-Wei Huang, associate professor of electrical engineering; Victor Bright, professor of mechanical engineering; PhD graduates Jan Bartos and Eduardo Miscles; and PhD student Jonathan Musgrave.

“Our work presents an opportunity where we can hopefully detect health conditions earlier and improve the lives of people,” said Gopinath.

Where zebrafish meets the eye

A cross-section image of the cornea and iris of a zebrafish eye. These images allowed CU researchers to verify that their OCT device can resolve structure in biological samples.

To test the device’s ability to perform biomedical imaging, the researchers turned to a surprising aquatic animal: zebrafish.

Zebrafish have been used in OCT research because the structure of their eyes is fairly similar to the structure of the human eye. For the study, the researchers focused on identifying where the cornea, iris and retina was from the zebrafish.

To conduct in-vivo or other bioimaginging, scientists need to be able to identify the structure of the samples of interest, such as the eye or organs inside the body. The two benchmarks that the group hoped to achieve were 10 micron in axial resolution and then around 5 microns in lateral resolution, all smaller than the width of a human hair.

“The interesting result was that we were able to actually delineate the cornea and iris in our images,” said Gilinsky. “We were able to meet the resolution targets we aimed for, which was exciting.”

Being able to test this bioimaging device can open new doors for mapping aspects of the retina that can be essential for diagnosing potential eye conditions like age-related macular degeneration and glaucoma.

Additionally, Gilinsky said, the new bioimagining technique could help in delineating actual human coronary features that would be important in diagnosing heart disease — the leading cause of death in the United States.

With the research team’s expertise in microscopy systems, they are hopeful to create endoscopes that could revolutionize bioimaging technology.

“There is a growing push to make endoscopes as small in diameter and flexible as possible to cause as little discomfort as possible,” he said. “By using our components, we can maintain a very small scale optical system compared to a mechanical scanner that can help OCT technologies.”

The project was funded by the Office of Naval Research, National Institutes of Health and the National Science Foundation.

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Two from ECEE earn AB Nexus grants for collaborations with CU Anschutz

Anonymous — Wed, 16 Nov 2022 16:52:54 +0000

Two from ECEE earn AB Nexus grants for collaborations with CU Anschutz Anonymous (not verified) Wed, 11/16/2022 - 09:52

Juliet Gopinath will tackle novel neurophotonics methods to access deep brain structures for decision making, while Zoya Popovic will advance technique for noninvasive brain temperature monitoring during cardiac surgery.

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Researchers make strides in commercializing simplified dual-comb spectroscopy

Anonymous — Tue, 30 Aug 2022 13:57:25 +0000

Researchers make strides in commercializing simplified dual-comb spectroscopy Anonymous (not verified) Tue, 08/30/2022 - 07:57

Emily Adams

Huang (left) and a graduate student discuss a project in their lab.

It is sometimes said that science is about truth, while engineering is about compromise.

With one laser project in his lab in the Department of Electrical, Computer and Energy Engineering, Shu-Wei Huang and his team are working on a compromise in order to find new applications for a powerful new technology and make it easier to commercialize.

As they looked at the innovative and extremely precise dual-comb spectroscopy being honed by mechanical engineering Associate Professor Greg Rieker and others, Huang’s team saw an opportunity to expand its applications.

“We've been trying to see whether we can compromise the performance a little bit to greatly simplify the architecture,” Huang said. “The application that we are especially interested in is the biomedical application because in biomedical applications, you don't need the same resolution you need to do something like methane detection.”

The result is the counter-propagating all-normal dispersion (CANDi) fiber laser, which won Bowen Li, a postdoctoral researcher in Huang’s lab, a prestigious award from Optica in 2021.

The key has been a redesigned laser cavity that allows for light to travel both clockwise and counterclockwise, which essentially makes two lasers out of one laser cavity. That, in turn, decreases the number of complex electronics needed to configure two lasers in dual-comb devices, Huang explained.

“We reduce the complexity in the laser design, and we have to compromise the precision a little bit, but it's still much better than the state of art tools used in biomedical applications,” Huang said.

In the team’s most recent Optica paper, they introduced new techniques to reduce the CANDi laser’s relative timing jitter, further proving that the laser will be a good option for a host of applications. That work won PhD student Neeraj Prakash a best poster award at Optica’s 2021 Laser Congress.

Huang said they’ve been working with a startup company in Taiwan that is interested in using CANDi for terahertz imaging – often used in screening for security and drugs. A lab at Colorado State University is also experimenting with the laser for Raman spectroscopy, which has applications in pharmaceuticals and water-quality monitoring.

“CANDi is a new fiber laser architecture and right now, we are working on several projects to unveil its full potential for dual-comb applications,” Huang said.

Read the Optica paper

Shu-Wei Huang and his team are working on a compromise in order to find new applications for a powerful new technology.

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Research collaboration explores multiple methods for brain imaging

Anonymous — Wed, 13 Apr 2022 20:31:33 +0000

Research collaboration explores multiple methods for brain imaging Anonymous (not verified) Wed, 04/13/2022 - 14:31

Researchers at the University of Colorado Boulder and Anschutz Medical Campus are exploring several imaging techniques aimed at creating lightweight miniature microscopes.

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Detailed time-lapse images of brain cells could lead to new insights for neurological disorders

Anonymous — Wed, 30 Mar 2022 13:52:56 +0000

Detailed time-lapse images of brain cells could lead to new insights for neurological disorders Anonymous (not verified) Wed, 03/30/2022 - 07:52

In the journal Biomedical Optics Express, CU researchers describe their new SIMscope3D, a miniature microscope designed for high-resolution 3D images.

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biomedical

���ӽ紫ý to host International Workshop on Biodesign Automation this June

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Researchers pioneer fluid-based laser scanning for brain imaging

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New optical technique could transform brain imaging in animals

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New bioimaging device holds potential for eye and heart condition detection

Where zebrafish meets the eye

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Two from ECEE earn AB Nexus grants for collaborations with CU Anschutz

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Researchers make strides in commercializing simplified dual-comb spectroscopy

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Research collaboration explores multiple methods for brain imaging

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Detailed time-lapse images of brain cells could lead to new insights for neurological disorders

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��ӽ紫ý to host International Workshop on Biodesign Automation this June