Blog

Follow the progress QSTORM research as it happens!

This unusual blog has multiple authors, including investigators and students from each of the four QSTORM university research labs.

> See Teams to learn more about the bloggers and their labs.

QSTORM-AO Phone Meetings – Update

Every four weeks the whole team gathers around phones in Boston, Ohio, and Georgia to update each other on the research and to troubleshoot problems.  The calls come into PI Carol Lynn’s conference line at the Museum of Science.  Carol Lynn she and Karine record notes to send out to everyone after the call.  QSTORM research associates (otherwise known as graduate students) take charge of reporting and sending images and data.   Here is a very brief update from July’s meeting:

The Georgia Optics team is in the midst of assembling their new STORM scope with capabilities for holographic and light sheet imaging that will give it 3D resolution, up to 10 microns in depth (most cells are only 7-8 microns across).   Abhijit runs computer simulations testing various design considerations for the hardware already on order.  He is also running image processing tests of nanoscale fluorophores placed in 3D helical patterns, to determine the specifications for the algorithms he will need to design to render the data cleanly.  In the meantime, the lab is using the existing system to run experimental studies with colleagues in bio.  One is studying the effects of the common cold virus on mitochondria and…

Kenya Alfaro is helping out in the Kner Lab this summer. She is a undergraduate double-majoring in biomedical and electrical engineering.

…REU student Kenya Alfaro has been lending a hand.

Meanwhile, the Ohio QDot team is building their own two-laser imaging test-bed, with counsel from Peter and the local Ohio State laser physics team.  The Winter Lab will use this tool to test their control of the new QDots they are designing with photo-activated “quenching switches” made of DNA and azobenezene linker molecules.  Abby and Kil Ho are troubleshooting all sorts of difficulties getting the DNA linkers to conjugate to the coated QDots they have synthesized for the task.

This phone call included a review of recent imaging papers and some in-depth discussion over various ways to isolate signal over background noise given that the QDots will need to be energized by visible light to stimulate linker molecule switching on and off, and also be activated by ultraviolet light to stimulate emissions from the QDot cores.

Meanwhile the MOS team is entertaining scads of summer visitors with the “Making Molecular Movies with QSTORM” presentation, and building content and structure for the new website.  Phone call participants liked the new mock-up pages they were sent, including new bio pages for each of them. MOS IT wizard Leah Brunetto says the site could go live by mid-August.

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Abby visits MOS!

This gallery contains 2 photos.

Abhilisha Dehankar was in Boston for the July 4th weekend, and took the time to tour the Museum and meet with the MOS QSTORM team.  She attended Karine’s “Making Molecular Movies with QSTORM” presentation and Megan’s presentation of “From Chemical more »

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Museum of Science web wizard Leah Brunetto has a surprise waiting for you.  The new QSTORM-AO website is coming.   In preparation, Leah has migrated qstorm.org to a new qstormlegacy.org domain.  Here’s a sneak peak at the new website banner:

 

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QSTORM meets Congress and NSF Director France Córdova

Jessica, Karine and I brought our whole PI squad, our first two-color QSTORM images, hands-on demos, and a Quantum Dot Peep Show to Capitol Hill last week and got a chance to speak with dozens of guests at “The Arc of Science” event sponsored by the National Science Foundation and the Coalition for National Science Funding.  NSF Director France Córdova spoke personally with us and later gave us a glowing review during  her welcoming remarks.  Chair of the House Science Committee Lamar Smith (R-TX), and Representatives Eddie Bernice Johnson (D-TX) and Rep Dan Lipinski (D-IL) also spoke to about 200 people gathered at the event, which showcased 11 NSF-funded

House Science Committee Chair Lamar Smith looking our way.

science projects (including LIGO) and our industry and community partners. We also met Robert Fleischmann, our QSTORM-AO program officer, James Olds, Asst. Director for BIO, and several other key NSF officials. We were proud to be able to share the QSTORM story with policy-makers and to help represent the power of basic and applied science to advance societal goals, and “enhance the US economy, security and global competitiveness” — the theme of the evening.

 

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QSTORM to Capitol Hill

QSTORM Heads to DC!

Members of the new Congress will learn about QSTORM at NSF’s Arc of Science event February 15, on Capitol Hill.  We are bringing our new quantum dot display kit and our gold-nanoshell DNA-linker model, plus lots of super-res cell images and even 6-foot cutouts of the whole PI team.  We look forward to sharing with lawmakers our quest to achieve pinpoint surveillance capability inside living cells.

Our new set of Quantum Dots for demonstration.

The NSF event will take place at the Raeburn building on Capitol Hill.

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QSTORM-AO FUNDED!

HELLO QSTORM FOLLOWERS:  WE ARE THRILLED TO ANNOUNCE THAT THE NATIONAL SCIENCE FOUNDATION AND A GROUP OF OUR PEERS HAVE AWARDED US FUNDS TO DEVELOP THE NEW QSTORM-ADAPTIVE OPTICS INSTRUMENT FOR SUPER-RESOLUTION IMAGING IN THICK TISSUE!

IDBR_PIsWe received the notice this week, and our award (DBI-1555541) begins immediately.   QSTORM-AO involves QSTORM veterans Peter Kner (University of Georgia), Jessica Winter (The Ohio State Univerisity, and Carol Lynn Alpert (Museum of Science, Boston), along with their colleagues and students.  The new instrument – to be built in Athens, Georgia – will use holographic imaging with advanced display technologies and new techniques for correcting distortions induced by light scattering in thick biological tissue.  At The Ohio State University, semiconductor nanotechnology will be combined with DNA origami to create intensely bright and switchable light emitters, individually targetable to selected molecules operating within biological systems.  This novel combination of high-precision technologies will provide investigators with unprecedented insight into critical sub-cellular biological processes within fruit flies and zebrafish and other model organisms important for biological research.   This close collaboration at the intersection of biology, physics, optics, and chemical engineering will provide a unique training opportunity for graduate student collaborators and it will be enriched with professional development in interdisciplinary science communication skills, provided by the Museum of Science team.   All team members will contribute to the development of the online team blog, lab notebook, and the QSTORM-AO website, in a quest to capture the instrument development process in real time, within a broader historical, scientific, and visual context.  Visitors to the Museum of Science will get weekly updates on the team’s progress, the NanoNerds YouTube Channel will carry podcast updates and the team will work with Emmy-Award winning NOVA producer Lawrence Klein to produce a short film on the quest to see more clearly and deeply into the mysteries of life.

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Farewell and Thanks!

It has been ten months since I left the QSTORM team, I was always thinking of writing something as a farewell. I was so fortunate to have the opportunity to work on this project as my postdoc research experience. I really enjoyed working in this team. Over the past three years, I had the chance to work on different aspects of this project including chemistry, biology and optics in three universities, it was such a wonderful experience to work in different interdisciplinary labs as well as live in three different cities during the whole project. I really enjoyed collaborating with the members of the QSTORM team in every lab. This endowed me not only the comprehensive and interdisciplinary expertise on super-resolution imaging, but also good communication ability and the team cooperation spirit.

I am now working at the University of Pittsburgh Cancer Institute (UPCI), continue working on super-resolution imaging. Different from QSTORM project, which aims to combine user-controlled quantum dots (QD) with STORM imaging and adaptive optics to create new super-resolution technique, my research now is trying to transform this technique to improve people’s life, by investigating breast cancer progression using STORM imaging, I would love to take this as a continuation of the QSTORM project. The experience and expertise I obtained from QSTORM benefit me a lot for what I am doing now, especially the experience of working in biology and optics labs.

The most exciting thing happened during the QSTORM project is that I became a father last year, my daughter just had her first birthday a few days ago and took her first step exactly that day, and she is walking better and better now. She is really a big change to our life, even though it was really tough for the first few months to take care of her. But we enjoy her growth much more, she surprises you every day with her new learned skills. I think such feeling is something you can’t understand until you became a parent by yourself, at least for me, I couldn’t imagine what it is to be a father.

Working in QSTORM was my first job in the US, also my first job in my life. Lots of amazing things during these three years and it means a lot in my entire life. I would like to thank this project and everyone in this team, I will always miss the time working in this project.

Best of luck with everyone, I look forward to working with you again.

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Kner lab publishes breakthrough applying genetic algorithm technique to adaptive optics for STORM imaging

Real-time wavefront correction with AO-STORM on Drosophila brain lobe. (a) wide field image, with area of interest outlined in white; (b) STORM image reconstructed after AO genetic algorithm reached optimized steady state.  Scalebars: (a) 2µm, (b) 1µm.  Doi: 10.1364/OE.23.013677

Real-time wavefront correction with AO-STORM on Drosophila brain lobe. (a) wide field image, with area of interest outlined in white; (b) STORM image reconstructed after AO genetic algorithm reached optimized steady state. Scalebars: (a) 2µm, (b) 1µm. Doi: 10.1364/OE.23.013677

Peter, Kayvan, Jianquan, and two of their colleagues at the University of Georgia have demonstrated the application of a”genetic algorithm” (GA) technique to adaptive optics (AO) to achieve a 4-fold increase in precision point-localization imaging through 50 microns of central nervous system tissue in fruit flies.  The breakthrough, published in Optics Express, combines advances in machine learning derived from mathematical models of evolution with methods for correcting optical wavefront aberrations derived from astronomy.  Imaging through layers of tissue produces distortions similar to  imaging through atmospheric layers, and this “thickness” problem has been one of the obstacles to achieving super-resolution imaging of molecules within living cells.  The GA technique allows the computer to sift rapidly through the thousands of variations in wavefront corrections generated by the adaptive optics algorithms and hone in on the “fittest” of these to prepare each of the image frames that will then be combined in the optical reconstruction process.  This is a big advance for STORM imaging, which, because of its reliance on sequentially recording randomized intermittent light pulses from fluorophore-tagged molecules, delivers light intensity fluctuations too extreme for traditional optimization techniques to handle.  Now that proof of concept has been achieved in a single 2D plane of central nervous system tissue, the team plans to move on to volumetric STORM imaging in which the image plane is stepped through the sample.  This will bring new challenges, but the authors note that “the GA approach is well-suited to correct these slowly varying dynamic aberrations and astigmatism can also be dynamically added for 3D STORM.”  See the full article and all images.

 

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2015 AAAS Symposium: Reunion in San Jose

IBIV at AAASJessica, Peter, Carol Lynn, and Karine reunited with other veterans of the 2010 NSF IBIV Ideas Lab last weekend in San Jose to engage in a spirited review of the  this unusual approach to stimulating high-risk, high-reward collaborative research.  None of us anticipated the quality and sheer quantity of scientific, career, educational, and societal impacts reported during this 3-hour session by PIs from all three imaging and visualization research projects funded through IBIV. NSF Senior Policy Advisor Chuck Liarakos, who briefed the audience on the evolution and goals of the Ideas Lab format, told the group near the end of the discussion that these summary stories had to find a way back to program administrators at NSF, either in writing or in briefings at the agency.   In a series of 15-minute talks, the PIs spoke of the great difficulty in forging productive working relationships with collaborators introduced to each other only during the five days of the intensive residential Ideas Lab, and also of their joy at achieving some breakthrough scientific results through these same collaborations, some still being played out.  Perhaps the most exceptional finding was of the enormous impact the IBIV funding had  on career development and directions for the relatively young set of investigators, some of whom received their first federal grant through this program.  The recently completed QSTORM student survey revealed profound implications for the 16 students and post-docs who participated for a year or longer, nearly all of them citing the benefit of the experience working on interdisciplinary teams in helping them pursue new paths in research and industry.  The model QSTORM pursued of hiring a roving post-doc, Jianquan Xu, whose year-long experience in three of the four labs spurred knowledge transfer and innovation, was well-noted by all present, including a UK research council attendee who indicated she would bring that concept back to her colleagues.  IBIV Ideas Lab facilitator Andy Burnett and IBIV PI Ed Rosa-Molinar noted how rewarding it was to get a chance to hear about some of the more profound and unforeseen consequences of this social engineering experiment in stimulating innovation which they helped to create.  Next steps?  Chuck Liarakos said he would like to find some way to capture the insights gained at this session in a further report, journal article, or meeting at NSF.   All participants agreed.

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Kner Lab Achieves Multicolor QDot 3D STORM! Paper in ACS Nano

ACS Nano Multicolor STORM image nn-2014-06952g_0009Congratulations to Jianquan, Kayvan and Peter on the acceptance of their paper, Multicolor 3D Super-Resolution Imaging by Quantum Dot Stochastic Optical Reconstruction Microscopy, in ACS Nano.

Abstract:
We demonstrate multicolor three-dimensional superresolution imaging with quantum dots (QSTORM). By combining quantum dot asynchronous spectral blueing with stochastic optical reconstruction microscopy and adaptive optics, we achieve three-dimensional imaging with 24nm lateral and 37nm axial resolution. By pairing two short pass filters with two appropriate quantum dots, we are able to image single blueing quantum dots on two channels simultaneously, enabling multicolor superresolution imaging with high photon counts.

See the paper here.

Comments

  1. Gang says:

    Hi Peter and Jianquan:

    Just saw your paper online. This should be a big part of the accomplishments of the QSTORM team; congrats!

    Gang Ruan

Posted in Kner Lab Notes, Team Blog | 1 Comment