June 2021
Real-time multi-angle projection imaging of biological dynamics manuscript published in Nature Methods!
We introduce a cost-effective and easily implementable scan unit that converts any camera-based microscope with optical sectioning capability into a multi-angle projection imaging system.
Find out moreDecember 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 hereNovember 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 articleAugust 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" articleJuly 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 techniqueNovember 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 publicationOctober 2019
ctASLM published
We present cleared tissue axially swept light-sheet microscopy, which allows subcellular, isotropic imaging in all clearing media.
Light-sheet microscopy of cleared tissues with isotropic, subcellular resolutionSeptember 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
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.
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.
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!
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.
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.
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.