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 August Phone Meeting

All teams met by phone yesterday and delivered updates.  

The OSU QDot team is wrestling with getting their Zinc Sulfide coated QDots ready for conjugation with their DNA linker molecule.  This linker will “switch” the dots on and off by regulating the proximity of a quenching gold nanoparticle.  But first, the QDots have to be transitioned out of their oily “organic” solution into a fully aqueous solution.  Abby reported that Step 1 of this process worked well: the ligand exchange from Trioctylphosphine (TOP) to Pyridine. But the second step, the ligand exchange from Pyridine to a multifunctional bonding peptide (Phytochelatin-3), failed.  The team laid out a number of routes to try to troubleshoot the problem.

3D Localization Test Simulation: Fluorophores positioned on a 5 micron radius helical backbone.

Down in Georgia, the Optics team is in the final stages of CAD-aided instrument design, and about to get a final part machined on campus before the build-out begins.  They’ve also been running some holographic STORM simulations to test the 2D and 3D localization accuracy of the current iteration of their image processing algorithm.  The results look good.  Next, Abhijit will add “density filtering” capacity to the algorithm. This will help the team screen out stray data points, like the ones you can see to the left of the helix above.

Here, Abhijit himself becomes a red data point against the majestic peaks of the Dolomites in northern Italy.

In other news, the MOS team launched the new QSTORM.org website and included another picture of Abhijit’s mountain adventures on his profile page.  Go to “Teams” to learn more about the people who are pursuing the QSTORM-AO quest.   Our next phone meeting is scheduled for September 21st.  Stay tuned.

Posted in Alpert Lab Notes, Team Blog | Comments Off on QSTORM-AO August Phone Meeting

The New QSTORM Site is Live at QSTORM.ORG!

We’re very pleased to make this announcement.  Soon, this blog will be renewed on qstorm.org as well.  Thanks to Leah Brunetto and the MOS Web team.

Posted in Alpert Lab Notes, Team Blog | Comments Off on The New QSTORM Site is Live at QSTORM.ORG!

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 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.

Posted in Alpert Lab Notes, Team Blog | Comments Off on QSTORM-AO Phone Meetings – Update

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 »

More Galleries | Comments Off on Abby visits MOS!

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:

 

Posted on by Carol Lynn | Comments Off on New Website Coming….

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.

 

Posted in Team Blog | Comments Off on QSTORM meets Congress and NSF Director France Córdova

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 presentations & hands-on activities.

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

Posted in Alpert Lab Notes, Team Blog, Winter Lab Notes | Comments Off on QSTORM to Capitol Hill

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.

Posted in Alpert Lab Notes, Team Blog | Comments Off on QSTORM-AO FUNDED!

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.

111hccfront

Posted in Jianquan Notes, Team Blog | Comments Off on Farewell and Thanks!

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.

 

Posted in Alpert Lab Notes, Kner Lab Notes, Team Blog | Comments Off on Kner lab publishes breakthrough applying genetic algorithm technique to adaptive optics for STORM imaging