DIY your own Programmable Illumination Microscope

The Fraden Group describes how to build your own Programmable Illumination Microscope in the American Journal of Physics

Have you ever marveled at the equipment used in a research lab? Have you ever wondered how a specialized piece of equipment was made? Have you ever wondered how much it would cost to build your own research microscope? Have you ever considered trying to make your own research microscope? The details on how the Fraden Group builds their Programmable Illumination Microscope for under $4000 was recently published in the American Journal of Physics.


The Programmable Illumination Microscope or PIM is a highly specialized microscope where the illumination for the sample being imaged comes from a modified commercial projector, nearly identical to the ones mounted in every classroom. For the PIM the lens that projects the image onto the screen is removed and replaced with optics (often the same lens in reverse) that shrinks the image down so that it can be focused through the microscope objective onto the sample. The light coming from the projector, which is the illumination source for the microscope, can be modified in realtime based on the image being captured by the camera. Thus the illumination is not only programmable but can also be algorithmic and provide active feedback.

This new publication in the American Journal of Physics, which is published by the American Association of Physics Teachers, is intended to help small teaching and research labs across the country develop their own PIMs to be built and used by undergraduate students. The paper includes schematics and parts lists for the hardware as well as instructions and demonstration code for the software. Any other questions can be directed to the authors Nate Tompkins and Seth Fraden.

7 Division of Science Faculty Recently Promoted

Congratulations to the following 7 Division of Science faculty members were recently promoted:

katz_dbDonald B. Katz (Psychology) has been promoted to Professor of Psychology. Don came to Brandeis as an Assistant Professor with a joint appointment in the Volen Center for Complex Systems in 2002 and was promoted to Associate Professor and awarded tenure in 2008. Don’s teaching and research serve central roles in both Psychology and the Neuroscience program. His systems approach to investigating gustation blends behavioral testing of awake rodents with multi-neuronal recording and pharmacological, optogenetic, and modelling techniques. Broad themes of the neural dynamics of perceptual coding, learning, social learning, decision making, and insight run through his work on gustation. For his research, Don has won the 2007 Polak Award and the 2004 Ajinomoto Young Investigator in Gustation Award, both from the Association for Chemoreception Sciences. Don has taught “Introduction to Behavioral Neuroscience” (NPSY11b), “Advanced Topics in Behavioral Neuroscience” (NPSY197a), “Neuroscience Proseminar” (NBIO250a), “Proseminar in Brain, Body, and Behavior II” (PSYC302a), “How Do We Know What We Know?” (SYS1c). For his excellence in teaching, Don has been recognized with the 2013 Jeanette Lerman-Neubauer ’69 and Joseph Neubauer Prize for Excellence in Teaching and Mentoring, the 2006 Brandeis Student Union Teaching Award, and the 2006 Michael L. Walzer Award for Teaching and Scholarship.

Nicolas RohlederNicolas Rohleder (Psychology) has been promoted to Associate Professor in Psychology. Nic is a member of the Volen Center for Complex Systems and on the faculty of the Neuroscience and Health, Science, Society and Policy programs. His course offerings include “Health Psychology” (PSYC38a), “Stress, Physiology and Health” (NPSY141a), and” Research Methods and Laboratory in Psychology” (PSYC52a). Nic’s research investigates how acute and chronic or repeated stress experiences affect human health across individuals and age groups. His laboratory performs studies with human participants using methods than span behavioral to molecular to understand how the hypothalamus-pituitary-adrenal (HPA) axis and sympathetic nervous system (SNS) regulate peripheral immunological responses and how these processes mediate cardiovascular disease, type 2 diabetes, and cancer, and aging. His research and teaching fill unique niches for all his Brandeis departmental and program affiliations. Nic’s research excellence has been recognized outside Brandeis with awards including the 2013 Herbert Weiner Early Career Award of the American Psychosomatic Society and the 2011 Curt P. Richter Award of the International Society of Psychoneuroendocrinology.

Matthew HeadrickMatthew Headrick (Physics) has been promoted to Associate Professor of Physics. He works at the intersection of three areas of modern theoretical physics: quantum field theory, general relativity, and quantum information theory. In particular, he uses information-theoretic techniques to study the structure of entanglement — a fundamental and ubiquitous property of quantum systems — in various kinds of field theories. Much of his work is devoted to the study of so-called “holographic” field theories, which are equivalent, in a subtle and still mysterious way, to theories of gravity in higher-dimensional spacetimes. Holographic theories have revealed a deep connection between entanglement and spacetime geometry, and Headrick has made significant contributions to the elucidation of this connection. Understanding the role of entanglement in holographic theories, and in quantum gravity more generally, may eventually lead to an understanding of the microscopic origin of space and time themselves.

Isaac Krauss

Isaac Krauss (Chemistry) has been promoted to Associate Professor of Chemistry. He is an organic chemist and chemical biologist whose research is at the interface of carbohydrate chemistry and biology. His lab has devised tools for directed evolution of modified DNA and peptides as an approach to designing carbohydrate vaccines against HIV. Krauss is also a very popular teacher and the recipient of the 2015 Walzer prize in teaching for tenure-track faculty.

Xiaodong Liu (Psychology) has been promoted to Associate Professor in Psychology. Xiaodong provides statistical training for graduate students in Psychology, Heller School, IBS, Neuroscience, Biology, and Computer Science, he serves as a statistical consultant for Xiaodong LiuPsychology faculty and student projects, and he performs research on general & generalized linear modeling and longitudinal data analysis, which he applies to child development, including psychological adjustment and school performance. He teaches “Advanced Psychological Statistics I and II” (PSYC210a,b), “SAS Applications” (PSYC140a), “Multivariate Statistics I: Applied Structural Equation Modeling” (PSYC215a), and “Multivariate Statistics II: Applied Hierarchical Linear Models” (PSYC216a). He is developing a new course on “The R Statistical Package and Applied Bayes Analysis”, and he recently won a Provost’s Innovations in Teaching Grant for “Incorporating Project-based modules in Learning and Teaching of Applied Statistics”.

Gabriella SciollaGabriella Sciolla (Physics) has been promoted to Professor of Physics. She is a particle physicist working on the ATLAS experiment at CERN in Geneva, Switzerland. Sciolla and her group study the properties of the newly discovered Higgs Boson and search for Dark Matter particles produced in high-energy proton-proton collisions at the Large Hadron Collider. Sciolla is also responsible for the reconstruction and calibration of the muons produced in ATLAS. These particles are key to both Higgs studies and searches for New Physics.

Nianwen Xue (Computer Science) has been promoted to Associate Professor of Computer Science.  The Computer Science Department is pleased to annNianwen Xueounce the promotion of Nianwen (Bert) Xue to Associate Professor with tenure. Since joining Computer Science he has made significant contributions to the research and teaching efforts in Computational Linguistics, including growing a masters program from zero up to 18 students this year. His publications are very well regarded, and focus on the development and use of large corpora for natural language processing, especially in Chinese. He has built a sizable lab with diverse funding that students from around the world are vying to enter.

Thank you to the following department chairs for their contributions to this post:

  • Paul DiZio, Psychology
  • Jane Kondev, Physics
  • Jordan Pollack, Computer Science
  • Barry Snider, Chemistry

Phi Beta Kappa Elects 51 Division of Science Students

Phi_Beta_Kappa_KeyThe Brandeis chapter of Phi Beta Kappa recently elected 97 new members. Of the 97, at least 51 undergraduate students are majors in the Division of Science (Biochemistry, Biological Physics, Biology, Chemistry, Computer Science, Mathematics, Neuroscience, Physics and Psychology).

Congratulations to the following new Phi Beta Kappa members from the Division of Science:


Malia Barbra McAvoy
Yehonatan Otzar Meschede-Krasa
Juhee Park
Lior Rozhansky
Hanchen Zhao (double major with Chemistry)

Biological Physics

Abigail Rose Knecht


Ignatius Ang
Zachary Ian Fried
Jenna Leah Kahane
Ariel Jennifer Katz
Yang Li
Yixuan Liao
Alice Yuan Meng
Khang Vi Nguyen (double major with Chemistry)
Danielle Marie Quintin
Sarah Shin


Khang Vi Nguyen (double major with Biology)
Soobyung Park
Noam Isaac Saper
Hanchen Zhao (double major with Biochemistry)

Computer Science

Kenneth William Foner
Huy Quang Mai
Grady Berry Ward (double major in Mathematics)


Cameron Zhang Fen
Trevor Weiss Kafka
Linda Li
Huy Quang Mai
Stefan Stanojevic
Zhengyang Zhou
Daniel Jackson Kutner (double major in Physics)
Murielle Claire Tugendhaft
Grady Berry Ward (double major in Computer Science)


Jessica Allison Haley (double major with Psychology)
Kiera Gillian Sarill (double major with Psychology)



Wei Zhong Goh
Stefan Stanojevic
Daniel Jackson Kutner


Kyra Jordana Borenstein
Hannah Dvorah Caldwell
Nicole Danielle Cardona
Avi David Cohen
Annie Cui
Jason Michael Desimone
Emily Rose Friedman
Jonathan David Gilman
Clara Emily Gray
Cecilie Gromada
Sarah Jessica Hack-Chabot
Jessica Allison Haley (double major with Neuroscience)
Jessica Lynn Lieberman
Danielle Mizrachi
Emily April Mostow
Linda Sue Nakagawa
Talia Michelle Portal
Jenna Louise Rice
Kiera Gillian Sarill (double major with Neuroscience)
Aliza Naomi Shapiro

See full story on BrandeisNow.

Jané Kondev wins the Lerman-Neubauer ’69 Prize for Excellence in Teaching and Mentoring

Kondev_labThe 2015 recipient of the Jeanette Lerman-Neubauer ‘69 and Joseph Neubauer Prize for Excellence in Teaching and Mentoring is Jané Kondev, Professor of Physics. This prize requires its recipient to be not only be an exceptional teacher, but also a person known to be an outstanding mentor and advisor.

Jané has advised first year students and majors, served on senior thesis and dissertation committees, and supervised undergrads, grads and post-docs working in his lab. Additionally, he had chaired the Physics department, served as chair and Undergraduate Advising Head of the Biological Physics program, and co-directed the Quantitative Biology graduate program. His courses include the first year seminar, “Nature’s Nanotechnology,” as well as “Advanced Introductory Physics,” “Biological Physics” and “Quantum Mechanics.”

Jané earned his BS at the University of Belgrade and his PhD at Cornell University, and a postdoc at Brown University, where he won two Excellence in Teaching Awards. The goal of his research at Brandeis is to develop quantitative models of biological structure and function that can be tested experimentally. His current projects include the study of cell-to cell variability in gene expression, homologous recombination in yeast, synthetic genetic circuits, and formin assisted actin assembly.

Jané’s research has been supported by grants from the National Institutes of Health, the National Science Foundation and the MIT Whitehead Institute. His co-authored undergraduate textbook, Physical Biology of the Cell, won the 2013 Society of Biology Book Award, and his articles have been published in such journals as the Physics Today, Genetics, Cell Reports, and Biophysics.

Students in his courses write:

“Jané is an awesome instructor. He really cares that the students understand the material.”

“I learned a lot from informal conversations with Professor Kondev, and I appreciate all the energy and passion that he brings to the classroom.”


Undergraduate Lab Tours Begin

Are you an undergraduate interested in gaining research experience by working in a lab at Brandeis? Not sure how to find a lab to work in?

The Biology Undergraduate Department Representative (UDRs) have created the Lab Tour Program. The first tour was held on Monday, April 13th. Lead by Biology junior, Sarita Biswas ’16, undergraduates toured the Dorothee Kern, Daniel Oprian and Chris Miller labs. Although a Biology major, Sarita has worked in Kern’s Biochemistry lab for nearly a year. During the tour, students were shown lab equipment and specialized research rooms (cold room, autoclave room) in the Volen Center. Throughout the tour, Sarita discussed the research that is being done in the labs.

Following the tour, Rashieda Pugh ’16 (UDR) and Sarita sat down with the students. Sarita discussed the kind of projects that she has worked on in the past year. Both Sarita and Rashieda shared their experiences in finding a suitable lab to work in, how they find a project to work on once in the lab, and the time commitment during the summer and academic year.

Some of the many questions asked:

  • Will there be a someone there to guide me? There is always a graduate student or postdoc mentoring you.
  • How do you find a lab to work in? Review the faculty webpages, find research that interests you and then email the professors. Do not write all the professors a generic email about opportunities in their lab. It’s unlikely to work. Take the time to find out what kind of research goes on in each lab. Target labs in which you have a genuine interest. Be prepared to show up in person and talk intelligently about research projects with the faculty member. Be prepared to emphasize what you have to offer – skills acquired in courses or other jobs, your dedication and willingness to apply yourself, your reliability and punctuality, your ability to communicate clearly and concisely, etc.
  • Is lab research considered an internship? Yes, it is very much like an internship.

Their advice is that there are a lot of labs here at Brandeis and a lot of ways to find rewarding research experience in a lab!

The Lab Tour continues on April 16th.

Rachel Woodruff Promoted to Assistant Professor

Rachel WoodruffRachel Woodruff has been promoted to Assistant Professor of Biology. Rachel joined the Brandeis faculty almost three years ago as an Instructor in Biology. During this time, Rachel has taught several Biology courses for undergraduate and Master’s students and recently guided Biology students as an Undergraduate Advising Head.

James Morris, Associate Professor, recently detailed Rachel’s importance to the Brandeis community:

“Rachel teaches courses for biology majors and non-majors. She regularly teaches Biology 14a-Genetics and Genomics, which is part of the introductory biology sequence. This course is taken by many first and second-year students. In addition, she teaches upper-level courses focusing on DNA damage and repair, as well as cancer, drawing on her research experience on DNA damage in bacteria and yeast. These classes include Biology 150b DNA Research and Mechanisms and Biology 172b Growth Control and Cancer. These seminar-style classes include opportunities to read and interpret scientific papers. She also teaches Biology 101b Molecular Biotechnology for advanced undergraduate and Master’s students, introducing students to techniques in molecular biology and teaching students to write their own research proposals. Finally, she teaches BISC 9b Biology of Cancer for non-majors, introducing this important topic to students in an accessible and engaging way.”


JBS Course Focuses on “Food, Lifestyle, and Health”

Elaine Lai, Senior Lecturer in Biology at Brandeis University, will be teaching a Justice Brandeis Semester (JBS) this summer titled Food, Lifestyle, and Health. The class runs from 6/1/2015 to 7/24/2015. The student receives 12 credits upon successful completion of the course. Food, Lifestyle, and Health will provide an immersive academic experience by combining academic training in the classroom with experiential learning in food labs.

The focus of this course will be to explore the link between food and health, specifically focusing on the factors that have lead to our national diabetes epidemic. Some of the issues studied will be the link between poverty and diabetes and diabetes and other chronic health conditions.

Applications for the Justice Brandeis Semester open on February 13, 2015. The application deadline is March 16, 2015.

JBS Offers “Bio-Inspired Design” Course

Maria de Boef Miara, Lecturer in Biology at Brandeis University, will be leading a course titled Bio-Inspired Design this summer (June 1 thru August 7, 2015). Bio-Inspired Design is part of the Justice Brandeis Semester (JBS). JBS combines courses and experiential learning to provide complete, immersive experiences so students can deeply examine a specific area of study.

Bio-Inspired Design is designed for students from a wide spectrum of disciplines, but may be particularly appealing to students in Biology, Biological Physics, Environmental Studies or HSSP areas. This is a 10-week course providing 12 credits.

Students in Bio-Inspired Design will spend the summer working with biologists, engineers and artists in a variety of settings. They will explore intriguing life forms and develop the quantitative tools needed to work at the intersection of form and function.

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