December 2020

Fiji annotation tool paper published

We have developed a useful Fiji plugin for the annotation of 3D data and movies in a user-friendly way. The plugin comes with a video tutorial. The paper with a detailed description and user guide is published in Biology Open.

The plugin can be found here

November 2020

Welcome to Conor, Shilpita, and Olwyn

Welcome to Conor McFadden, Shilpita Mitra-Behura, and Olwyn Doyle! Conor will support the Fiolka Lab in its push for new microscope technology and will be shared with the lab of Dr. Kevin Dean. Shilpita and Olwyn are part of the U-Hack Med Gap Year program of the Department of Bioinformatics and will work on bringing more computational power to our research as research interns. Welcome!

September 2020

Systematic Analysis of lattice and Gaussian light-sheets

Our systematic and quantitative analysis and comparison of lattice and Gaussian light sheets have been published! We find that square lattices are very similar to Gaussian-based light sheets in terms of thickness, confocal parameter, propagation length, and overall imaging performance.

Read the Optics Express article

August 2020

"In Pursuit" Article

UT Southwestern's Magazine "IN PURSUIT" spotlights the advanced microscopes developed by Kevin Dean's lab and our lab.

Read the "In Pursuit" article

July 2020

EDF-mask paper published

We present a new method to extend the depth of focus in two-photon microscopy by splitting up an ultrafast laser pulse into multiple annular beamlets. Compared to other methods, our technique has high light throughput, is achromatic, and is easy to implement.

Read about our technique

November 2019

C-light-sheet paper published

We are very happy to announce that our latest publication Light-sheet engineering using the Field Synthesis theorem by Bo-Jui Chang & Reto Fiolka has been published in the Journal of Physics: Photonics. We leverage the recently discovered Field Synthesis theorem to create light-sheets where thickness and illumination confinement can be continuously tuned. Explicitly, we scan a line beam across a portion of an annulus mask on the back focal plane of the illumination objective. Since the scanning pattern on the back focal plane looks like a letter C, we chose to call them C-light-sheets. We experimentally characterize these light-sheets and we found the C-light-sheets tend to generate a better image in terms of resolution and contrast compared to the Bessel, Hexagonal lattice, and Square lattice light-sheets.

Read the publication

September 2019

3D motif detector paper published!

Our latest publication, ​Robust and automated detection of subcellular morphological motifs in 3D microscopy images by Meghan K. Driscoll, Erik S. Welf, Andrew R. Jamieson, Kevin M. Dean, Tadamoto Isogai, Reto Fiolka & Gaudenz Danuser, has been published in Nature Methods. Here, we describe a computational workflow for investigating the coupling between 3D cell morphology and intracellular signaling. In particular, we introduce a generic morphological motif detector that uses machine learning to find morphological structures, such as lamillipodia, blebs, and filopodia, given user-provided examples of these structures. Although this workflow can be used on images from a wide variety of microscopes, it was specially designed to be used on images from high-resolution light-sheet microscopes.

Read the paper
Dr. Bingying Chen

September 2019

Dr. Bingying Chen joins the Fiolka Lab!

Bingying Chen joins the Fiolka Lab from the School of Electronics Engineering & Computer Science, Peking University​. She will work on nonlinear microscopy and its applications at UT Southwestern. Welcome!

February 2019

Field synthesis paper published!

We are very happy to announce our latest publication Universal light-sheet generation with field synthesis. by Bo-Jui Chang*, Mark Kittisopikul*, Kevin M. Dean, Philippe Roudot, Erik S. Welf & Reto Fiolka has been published in Nature methods. We introduce field synthesis, a theorem, and a method that can be used to synthesize any scanned or dithered light sheet, including those used in lattice light-sheet microscopy (LLSM), from an incoherent superposition of one-dimensional intensity distributions. Compared to LLSM, this user-friendly and modular approach offers a simplified optical design, higher light throughput, and simultaneous multicolor illumination. Further, field synthesis achieves lower rates of photobleaching than light sheets generated by lateral beam scanning.

A Nature Methods Commentary is also available that describes the novel approach to light sheet generation.

*These authors contributed equally.

Read our field synthesis paper
Stephan Daetwyler

September 2018

September 2018 News

Stephan Daetwyler started as a postdoctoral researcher in the Fiolka Lab. He is an interdisciplinary scientist with a major in Biology and Physics​ from ETH Zurich. He will combine advanced light microscopy with custom data processing to study human diseases in the Zebrafish model. Welcome, Stephan!

August 2018

August 2018 News

Reto gave an invited talk at the 10th-anniversary light-sheet fluorescence microscopy conference in Dresden, Germany. He presented for the first time his new Field Synthesis theorem that allows flexible light-sheet generation.

April 2018

April 2018 News

Spring was a busy season for the Fiolka Lab:

Tonmoy Chakraborty started as a postdoctoral researcher in the Fiolka Lab. He will be working on adaptive optics and cleared tissue microscopy.

Reto was invited to the Calico Lab in San Francisco to present our work on quantitative cancer cell imaging in 3D micro-environments.

Reto and Kevin attended the focus on microscopy conference in Singapore. Reto presented our work on light-sheet microscopy and adaptive optics and Kevin presented his research on 3D morphodynamics, actin regulators, and Cell-Matrix adhesions.

March 2018

NIH Pathway to Independence Award

Postdoctoral researcher Meghan Driscoll has been awarded a Pathway to Independence Award (K99/R00) from the National Institutes of Health. The grant is designed to facilitate the transition of outstanding researchers from mentored, postdoctoral research positions to independent, tenure-track, or equivalent faculty positions. The award will provide over $900,000 over five years to support Driscoll's research program that focuses on how cells migrate through and interact with complex 3D environments.

Driscoll has devoted her research efforts to developing computational tools that allow scientists to overcome the technical challenges associated with the quantitative analysis of 3D cellular processes. Cell migration is critical to many physiological and pathological processes, including embryogenesis, wound healing, immune function, and cancer metastasis. The Pathway to Independence Award will allow Driscoll to further develop and use light-sheet microscopy techniques to quantify cell migration in 3D collagen matrices. Breakthroughs in this field require the synthesis of knowledge and techniques from several academic disciplines. Driscoll's highly interdisciplinary background, and current research environment, include close collaborations with physicists, applied mathematicians, electrical engineers, chemists, computer scientists, and cell biologists. This has allowed Driscoll to develop a unique combination of skills as a physicist with mathematical talent and with a deep understanding of the biological processes, that have equipped her to become a pioneer in the new 3D cell biology era.

January 2018

January 2018 News

Kevin Dean, Ph.D., a postdoctoral Researcher in the Department of Bioinformatics mentored by both Gaudenz Danuser, Ph.D., and Reto Fiolka, Ph.D., will receive the 2018 Dean’s Discretionary Award. Dr. Dean developed light-sheet microscopy methods that enable quantitative subcellular imaging and then combined the strengths of these one-of-a-kind microscopes with computer vision and genome editing to elucidate the contribution of specific actin regulators on cell morphodynamics and migration in 3D extracellular matrix environments.

Etai Sapoznik

December 2017

Welcome Etai!

Etai Sapoznik started as a postdoctoral researcher in the Fiolka Lab. He is a bioengineer by training and will work on collaborative and interdisciplinary research projects involving microscopes developed here at UTSW. Welcome, Etai!

Bo-Jui Chang

September 2017

Welcome, Bo-Jui Chang!

Bo-Jui Chang started as an instructor in the Fiolka Lab. Bo-Jui is an expert in light-sheet microscopy and structured illumination and will be involved in designing and building the next-generation optical microscopes at UTSW. He will also help maintain and upgrade the existing light-sheet microscopes that we have built.

August 2017

August 2017 News

Light Sheet Development:
Reto visited the lab of Dr. Jan Huisken at the Morgridge Institute for Research in Madison, WI, and gave a talk about our light sheet development.

New Concept to Parallelize 3D Acquisition of Light Sheet Microscopes:
Congratulations to Kevin Dean on his publication in Nature Scientific Reports. The work presents an approach to parallelizing the 3D image acquisition process of digitally scanned light sheet microscopes (DSLM). Since the parallelization process does not involve additional light losses, this method has the potential to speed up 3D image acquisition.

Read Kevin Dean's Publication

April 19, 2017

Quantitative Cancer Cell Biology Talk

Reto gave an invited talk at the "Scientific Center for Optical and Electron Microscopy" at ETH Zurich. He presented our work on quantitative cancer cell biology in 3D using advanced imaging technology.

April 9, 2017

Focus on Microscopy

Reto gave a keynote talk at the opening session of the Focus on Microscopy conference in Bordeaux. He presented our ongoing work on light-sheet microscopy for quantitative cell biology.

April 3, 2017

Frontiers in imaging science

Reto gave a talk at the Frontiers in Imaging Science conference at Janelia Research Campus. He presented the work in the Fiolka Lab on accelerating 3D imaging by paralyzed acquisition.


February 2017

Latest manuscript published and selected as cover of Optica

Increased imaging speeds in 3D fluorescence microscopy through parallelization

Congratulations to Kevin Dean for publishing our latest work in Optica (Vol. 4, Issue 2) and contributing the cover image of the current issue. Through parallelization, we report threefold faster imaging speeds in 3D fluorescence microscopy while maintaining the same light dosage and sensitivity of a conventional, slower microscope. This enables long-term, high-speed, and high-resolution volumetric imaging of biological processes that included cell migration, vesicular trafficking, and neuronal action potentials.

Read our latest manuscript
Grazing cell

December 2016

New TIFR Technique Published

New TIRF technique with improved background rejection published in Optics Express

Using a combination of structured illumination and TIRF microscopy, Reto Fiolka demonstrated improved optical sectioning in TIRF microscopy. In addition, the same setup and optical trick can also be used from HILO microscopy, an operating mode that helps to image deeper into cells when using a TIRF setup. This work is now published in Optics Express, Vol. 24, Issue 26.

Read the about the new technique