Imaging Course

Visitor of the Week: Tuce Tombaz


Meet Tuce Tombaz of the Norwegian University of Science and Technology (Norway). The Turkish national is a Ph.D. candidate within the Kavli Institute for Systems Neuroscience and is currently training at our three-week summer course on Imaging Structure & Function in Nervous System. This is Tuce’s first course at CSHL, and she is our second trainee this summer hailing from Jonathan Whitlock’s lab.

What are your research interests? What are you working on?
My general interests cover a variety of topics spanning sensory and motor explorations in systems neuroscience. My work focuses on how rodent brains represent different aspects of behavior, and this interfaces with social cognition. More specifically, I investigate whether individual cells represent performed and observed actions similarly, a finding which could pave the way for understanding the neural bases of social learning.

How did you decide to make this the focus of your research?
Initially, I didn’t know. I have a background in molecular biology and genetics. I was interested in microscopy techniques to visualize things that are not visible to the naked eye. I have spent quite a of bit time in different labs to learn more about different methods that aim to answer different questions. I became very interested in my current project when I first read about it in the job description. It allows me to use imaging techniques to look for something fundamental to the animals’ experience.

How did your scientific journey begin?
I can’t specify an instance that inspired me, but having worked in multiple labs throughout my career enabled me to complete a combination of projects I completed that made me more curious about novel questions. I really enjoyed the collaborative aspects of these projects and thinking about how to solve difficult problems. It was initially at the molecular level and now at the behavior level.

Was there something specific about the Imaging Structure & Function in the Nervous System course that drew you to apply?
Yes, I knew that there is no other course which could teach so much about imaging techniques than this course. It is quite common that, during the span of the graduate program, you are extremely busy with acquiring data such that you are often unaware of the operative details of the system you are using. I was always curious to know how the system works and that fundamentally requires you to dismantle and assemble a microscope. During this course, I was able to set up multiple imaging systems from scratch and learn the theory behind them. I understand that the knowledge I will gather throughout the course will be invaluable, so I feel privileged to be here.

Though you’re only one third of the way through the course, what have you so far learned from it that you can apply to your work?
So far, I have learnt the very basics of optics, different types of imaging setups and how they are used. I also built wide-field and fluorescence microscopes. This knowledge can already be transferable because we don’t learn about any of these in graduate school and how it could all affect our data. By the end of the course I will be able to learn how to combine certain imaging systems with the optogenetic manipulations that would certainly be important for my project and also other projects in the lab.

Do you already have a takeaway from the course that you want to share?
It is really hard to pinpoint one so I will name two:

  1. Know your imaging setup completely; what the bits and pieces are and what could potentially make a big difference.

  2. Design the imaging setup according to your needs.

Both of these would give you a sense of what might be wrong with your imaging.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I would highly encourage motivated scientists to attend this course. It is a very useful course if one is curious about how to build scopes for effective usage. I should also add that the course is intense. You will get to learn so much in a very short period of time.

What do you like most about your time at CSHL?
Meeting new people was definitely one of the highlights of this course. The campus is also very pretty.

Tuce received financial support from Howard Hughes Medical Institute (HHMI) to cover a portion of her course tuition. On behalf of Tuce, thank you to HHMI for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Tuce for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here.

Visitor of the Week: Nick Weilinger


Meet Nick Weilinger of the University of British Columbia (Canada). The postdoctoral fellow is a member of Brian MacVicar’s lab in the Centre for Brain Health and is on campus training at his first CSHL course: Imaging Structure & Function in the Nervous System

What are your research interests? What are you working on?
My work focuses on understanding how the brain swells (called cerebral edema) during stroke and traumatic brain injury. I approach this by imaging movement of chloride ions, which are crucial in controlling the volume of nerve cells by regulating their solute content. 

How did you decide to make this the focus of your research? 
Despite cerebral swelling being a hallmark consequence of brain trauma and a major cause of death in patients with large infarctions, we have no direct way to treat the underlying changes in cell volume. In the MacVicar lab, we are highly motivated to identify novel targets for therapeutic intervention. We have developed new ways of measuring the chloride changes that trigger cell swelling under these conditions, and hope to pinpoint the key routes of chloride entry as potential drug targets. 

How did your scientific journey begin? 
I kind of fell into it. I didn’t know what to do after undergrad, so I looked back on which courses interested me most; and my neurobiology courses stood out. I was lucky to start as a MSc student in a terrific lab without any prior experience and that led to a PhD in Neuroscience! 

Was there something specific about the Imaging Structure & Function in the Nervous System course that drew you to apply?
The neuroimaging course provides students with a unique opportunity to build custom microscopes: advanced microscopy theory can be taught anywhere, but getting hands-on experience with all the equipment needed to build a microscope from scratch is a rare thing. 

What and/or how will you apply what you've learned from the course to your work? 
My classmates and I will be leaving this course with the practical know-how to build, repair, and modify microscopes to answer niche scientific questions that would otherwise be difficult to address. I am confident that I will be well-positioned to teach my labmates what I’ve learned here so that we can improve upon our data acquisition methods. 

What is your key takeaway from the course?
CSHL brings in a world-class lineup of lecturers and teaching assistants who are on the leading edge of their respective fields. Not only did the course offer tremendous learning opportunities, but the one-on-one interactions over the past weeks have fostered a new network with both instructors and students. I leave campus with new colleagues whom I look forward to collaborating with throughout my career. 

How many CSHL courses have you attended? Will you be attending another CSHL course or meeting in the near future?
This is my first time at CSHL and I don’t have anything else scheduled, but after visiting the campus firsthand I can say that I will certainly return for a future meeting! 

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
The neuroimaging course was personally recommended to me by colleagues who have attended in the past. It is a fully immersive, challenging and, most importantly, fun experience. I would not hesitate to recommend the neuroimaging course to a colleague.  

What do you like most about your time at CSHL?
What stood out to me the most was developing new friendships with trainees from across the globe - and enjoying a frisbee/football break at lunch!

Thank you to Nick for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here.

A Word From: Florin Albeanu, Michael Orger, Lucy Palmer & Philbert Tsai

L to R: Ken Zaret, Fiona Watt, Marius Wernig; Photo by Constance Brukin

Last summer, the twenty-seventh  annual course on Imaging Structure & Function in the Nervous System was held at Cold Spring Harbor Laboratory. We chatted with the 2017 co-instructors Florin Albeanu, Michael Orger, Lucy Palmer, and Philbert Tsai to gain an inside look into the long-running, intensive course  First, we asked about a day-in-the-life of an Imaging trainee, and learned they literally build microscopes from scratch during the three-week course: 

Phil: The typical daily schedule changes from week to week but overall, we try to avoid an information overload. For example, in the first week, we don’t like to bombard the trainees with a lot of information all at once so the schedule is kind of lecture, practical, lecture, practical. The practicals are lab bench exercises that allow the students to tinker with stuff and effectively learn how to build a microscope from scratch. 
We begin at 9 AM with three hours of lectures on the fundamental of optics and methods of microscopy to ensure everyone has a good foundation of the basics. After lunch, the students spend two to three hours working on optical bench rails and building small imaging systems. The systems become more complicated with each practical, from simple lens imaging to a full wide-field microscope to a laser scanning microscope (which is a bonus for some students because it can be turned into a confocal microscope). Later in the afternoon, we have another lecture that is oftentimes followed by questions that came up during the practical. There are questions the students will only ask if they’ve actually been confronted with the fact that something doesn’t work the way they thought it would; if we jumped from one lecture to the next without a practical in between, those questions would not come up and the depth of conversations would not be the same. By the end of the first week, the students move into the main lab and start working with million-dollar microscopes, at which point they have a better idea of what’s going on behind the lens. 
Michael: As the students transition from the optical bench exercises to the microscope, the first step is to conduct experiments designed to better understand the fundamental principles of what they’ll do in their own work. They measure the noise characteristics and resolution of the microscopes so they understand the possibilities and limitations in their experiments in a very general way. When they’re using the microscopes in the course, they’re really learning how to understand the measurements they’re making and what they mean.
Florin: During the second and third week of the course, there are a lot of applications of the basic ideas taught in the first week. And in many cases, the trainees realize that exactly the same concepts are packaged in different microscopes. Fancy up-and-coming microscopes, in fact, use the same two or four lenses again and again. 
Lucy: In the third week, the students also work on their own course projects, which they can pursue solo or as part of a group.
Michael: The final assignment of the course, right before the lobster banquet, is for the students to present the results of their projects or anything else they want to share regarding what they learned during the course. 
Phil: Outside of the course projects, we always have them work in at least pairs because we feel the social aspect is important. When the students do the optical bench exercises, they work in groups of 3 or 4 which indirectly becomes a team building exercise. A majority of students never thought that they could build a microscope. So there’s this team effort to overcome the hurdle of “We’re supposed to build a microscope from scratch in three hours? No way!” And they all end up doing it. 
Florin: They also realize that the microscopes they build, in many cases, can do as good a job as the pricey microscopes on the market. That knowledge goes a long way. If funding is a limitation, they have the experience to build their own microscope and understand exactly how everything works in it. 
Phil: The microscopes the students build use $40 lenses and $50-100 scanners, so they do have certain limitations. They’ll never be as good as a well-engineered, million-dollar microscope, but a homemade version can get you 95% of the way there. The critical thing is realizing what that last 5% is and whether it’s worth hundreds of thousands of dollars. When you’re doing cutting edge research, it’s important to understand where the critical components are so you know where to spend your money and where not to waste it.
Florin: Getting the students to play with the lenses themselves actually makes this much more obvious. More than that, as you look at the microscope, you realize the precision of the microscope is the precision of your hands, of your alignment, and that’s empowering. 
Michael: The students also have the opportunity to try new things and test out ideas. We have a combination of commercially built equipment--a lab of ten of the nicest microscopes at their disposal--and equipment just for developing and trying new things. Very often, actually, the course projects aim to make a particular method a little bit better. 
Phil: Microscopy is one of those topics that falls between traditional departments. On the physics side, the basics of how a microscope is constructed are taught but most physics departments don’t teach their undergraduates about laser scanning microscopes or confocal microscopes. Biologists, on the other hand, use these microscopes all the time but are unfamiliar with the working principles behind the microscopes. Over the years, alumni have told us they don’t know where else they could have learned all this, that the course is the only place they could find all this information.
Florin: Also, a physics book on optics can be a little dry. So if you are a biologist trying to understand imaging, learning through a book can be a long path. Being part of a course like this exposes you to all kinds of tools, principles, and techniques in optical imaging, then you actually use them to build a device.
Michael: You can read a book about optics but until you get your hands on things, it’s really hard to fully grasp the concepts.

Invited speakers play a major role in CSHL courses, including the Imaging course. Next, the instructors discussed the caliber of the 2017 speakers and their contributions to the course and its trainees. 

Michael: We schedule the invited speakers on a bit of a gradient: speakers at the beginning of the course cover basic methodologies and those toward the end talk about more specific applications. Our speakers are really, really great. A number of them have been coming to the course for over a decade, possibly even two.
Phil: And they evolve. Their talks are always on their most recent research as well as what they’ve done in the past. We invite them back because they enjoy this crowd and its interactive-ness. These are conference-level speakers who give colloquia to departments or universities in front of hundreds of people. The course trainees get to be in the room with them, have lunch with them, and ask them whatever questions they have. That’s a real opportunity.
Michael: It’s a completely different experience than if the person came to your university and gave a talk. In the course, the students can really ask the speakers whatever they want. And almost all of the speakers like to stay at the course for extended periods to spend time with the students.
Phil: Many of our speakers are the ones who started this field.  
Florin: Sometimes new projects arise from these interactions; course alumni have joined the labs of invited speakers they met in the course.
Phil: Let me phrase it this way: it’s the chance for an interaction that sometimes changes the course of a career. It’s the types of conversations that are had in a crowd of 12 people, in an atmosphere that encourages questions, ideas, and curiosity. There have been times when a student might ask, “I’m interested in X. Could X be used for Y?” And when a person who created X and uses it every day answers with, “Actually, X would be ideal for Y,” it’s very encouraging. The student follows a new research direction because of that one exchange. 

We then asked how the course has changed over years:

Lucy: Phil is probably the best person to answer since he’s been with the course for 15 years.
Phil: I’m the best and worst person to answer this because I have a terrible memory! Fundamentally, I think the course hasn’t changed that much over the last 15 years. This biggest evolution has been fine-tuning the iterative back-and-forth of listening to lectures, followed by tinkering in the lab practicals, followed by more lectures and Q&A sessions. I think we’re in a pretty good place with that now. 
Lucy: The course content also evolves as new approaches come out. We really try to stay on top of the field with different preps and techniques, so the students are always exposed to cutting-edge material. 
Phil: More and more students are coming to the course with the word ’microscopy’ already in their background. Ten to fifteen years ago, students applied to the course because imaging was becoming big and was gaining momentum in the field of neuroscience – but not everybody was yet doing it. Today, imaging is starting to dominate. You’ll be hard-pressed to find a core facility or university without a two-photon microscope. As a result, the students now have some prior two-photon imaging or confocal imaging experience, and they want to learn what’s going on inside the microscope when they adjust settings. So the things we teach in the first week haven’t changed much. And despite students having done microscopy at their home lab before arriving at the course, they still gain quite a bit from the material taught the first week. 
Michael: I think there’s been an increased focus on in vivo preparation. When I was a student of this course in 1999, there was a lot of cell culture and various other preps. But imaging activity on the cortex of a mouse was not something we did.
Phil: It was more limited to in vivo slices and cell cultures.
Lucy: Synthetics.
Florin: Funnily enough, things that were talked about in the course 10 to 15 years ago as dream projects are actually being done now in the class by students. And we still talk about “the new dream experiment” that will probably be implemented in the next decade by people involved in the course now. 

As one of our most competitive courses, we made sure to inquire how applicants might increase their chances on becoming one of the 14 to 16 scientists each summer who are accepted into the course. 

Michael: We look for applicants who are new to imaging and understand some of the problems they’re facing, but don’t yet fully understand what they’re doing. We want to train people who will be able to return to their labs and quickly take advantage of what they learned in the course. A lot of information is taught during the three weeks so it’s important that students can attend the course, understand why they’re learning what they’re learning, and go back to their labs to directly apply their newfound knowledge. This way, the information is reinforced as soon as possible. 
Florin: We also look for applicants who are about to switch fields or start a new project. 
Michael: We try to accept a mixture of students in terms of scientific background. We have had some students from physics backgrounds who have never seen a biological specimen, but have a firm understanding of how some elements of microscope systems work. And vice versa. It’s great to have a mixture like that because the students learn not just from the instructors, speakers, and TAs, but from each other. They can ask each other questions and share their knowledge. 
Applicants’ personal statements should really express how the course is going to benefit their experiments or, even further, their labs. Of course, we want students with great scientific backgrounds, but the personal statement is less about selling yourself as a scientist and more about how this course is going to help you to do science better. For example, if you’re in a lab that is just starting to set up imaging but doesn’t have an electrophysiologist, that student’s participation in the course will have an impact even beyond their own research projects. 
Another important thing to note is that every year we reject a bunch of great students. If you really want to take this course and think this is what you need, don’t give up. We consider persistence a big positive. So if an applicant states “I applied last year and didn’t get in and now I’m applying again,” it catches our attention. Besides wanting a group of motivated students who are fun to work with and enthusiastic about the experiments, we want people who really want to take the course.

Our chat closed with the co-instructors answering, “What’s your favorite moment from the course?” 

Florin: It was my first encounter with the course. In 2006, I came in as a TA and was supposed to build a device in a short amount of time. Clearly, I was terrified dealing with the parts, but the instructors at that time said, “don’t worry, it’s going to work out just fine.” And indeed it did. Here, you are surrounded by extremely enthusiastic people whose encouragement makes a lot of things happen in a very short amount of time. 
Phil: My favorite moment happens every year and it changes in flavor: it’s that moment when the students, who have been working on a rig for hours, struggling with noise and all sorts of other stuff, finally obtain a fluorescent image. They put together this scanning microscope themselves from a table of random parts and spent an hour aligning it, and now they see a high-quality image. They literally scream and jump for joy. They’re taking pictures of their microscopes and the image with their phones, posting it on Facebook, texting it to their loved ones and colleagues. It’s the excitement of realizing that they’re capable of something they didn’t know they were capable of just a few hours ago. 
Michael: A lot of great moments happen throughout the course but one thing that is a pleasure to see takes place some years after a student’s been in the course. I see them post on Facebook about their new publication, and actually see the imaging they came to the course to learn. It’s always very satisfying to be reminded that the course has an impact on the students beyond just the three weeks. 
Lucy: I have quite a lot of favorite moments from when I was a student in the course, and now as an instructor. As a student, it was building my own two-photon which was amazing: I was elated when I took the image. And now as an instructor, my favorite part is seeing all the students get to that same pinnacle and realizing they can do it. I enjoy seeing the motivation and excitement in students when they’re able to address a question they’ve always wanted to address. 

The Imaging Structure & Function in the Nervous System course this summer will take place between July 24th and August 13th. Applications are being accepted until this Sunday, April 15th here. For an introduction into the course from a trainee, be sure to read our Q&A with 2017 Alumna Janani Sundararajan

For more conversations with other course instructors, check out the rest of our A Word From series. 

Visitor of the Week: Janani Sundararajan


Meet Janani Sundararajan of Duke University. A graduate student in Richard Mooney's lab, Janani is on campus for the Imaging Structure & Function in the Nervous System course where she is gaining hands-on experience on the latest imaging techniques and technologies from the ground up. 

What are your research interests? What are you working on?
I am currently working on how movements affect our ability to hear and the neural circuitry underlying changes in auditory perception during resting and movement.  

Was there something specific about the Imaging Structure & Function in the Nervous System course that drew you to apply? 
I was most interested in learning about the latest imaging techniques in neuroscience that I could apply to my work. I particularly wanted to learn more about intrinsic imaging, calcium imaging and photo stimulation techniques to look at the activity of different subpopulations of auditory cortical neurons in different behavioral states.

What is your key takeaway from the course?
I have learnt a lot of concepts in the course that are directly applicable to my current and future work. The course focuses on training students on both the basics of optics and the current cutting-edge imaging techniques in neuroscience including confocal and 2-photon microscopy which are very useful to my research work. It has also given me the opportunity to try out these techniques in the practical sessions and learn about digital image processing methods.

How many CSHL courses have you attended? How about CSHL meetings? 
This is my first CSHL course. I am really enjoying it so far and hope to attend a CSHL meeting in the future.

If someone curious in attending your course asked you for feedback or advice on it, what would you tell him/her?
I would absolutely encourage anyone interested in this field to take the course. A great thing about the course is that it is very interactive. The course itself is interactive and we are presented with opportunities to meet and speak with a number of experts in the field. 

What do you like most about your time at CSHL?
The casual environment which lets you interact with other members in the scientific community. Also, the scenic location of the campus with the harbor on one side and greenery on the other is very beautiful and refreshing.

Janani received a stipend from the Howard Hughes Medical Institute (HHMI) to cover a portion of her course tuition. On behalf of Janani, we would like to thank HHMI for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network. 

Thank you to Janani for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course – go here.