Education

University of Cambridge, Cambridge, UK (Sep ’22 – Present)

PhD in Neurosciences

University College London, London, UK (Sep ’16 – Jun ’20)

MSci in Natural Sciences (Physics and Molecular Cell Biology), 1st Class Honour

My coursework included modules on mathematical and computational modeling, advanced statistical methods and biophysics, electromagnetism theories, quantum physics, and condensed matter physics. For my final year thesis, I worked on automating open-source microscopy. I also participated in a one-year exchange program at McGill University in Montreal, Canada during my third year of study.

Skills

Development tools

Prior experience in using Arduino, Raspberry Pi and Altera FPGA boards

Programming Language

Previous experience in using Python for data acquisition and analysis, parallel processing, instruments control and building simulations. Confident with MATLAB and Bash scripting. Familiar with C, Kotlin (Java-based) and Verilog HDL.

Human Language

Native in Mandarin and Japanese. Fluent in English.

Research Experiences

Research Assistant at Academia Sinica, Taipei, Taiwan (Jan ‘21 – Sep ‘22)

Optical Microscopy work
At Dr Bi-Chang Chen’s lab, I automated manual image segmentation tasks on light-sheet images using the open-source ML software (e.g., Cellpose) and custom Python/ImageJ script. I also mentored a summer student on an image processing project.

Co-authored a review paper: “Lu, C.-H., Huang, C.-Y. et al. Large-scale expanded sample imaging with tiling lattice lightsheet microscopy. Int. J. Biochem. Cell Biol., 154, 106340 (2023)”

Electron Microscopy work:
At Dr Shang-Te Hsu’s lab, I established the first high-resolution cryo-tomography processing pipeline in Taiwan. This involved a comprehensive understanding of existing open-source packages, extensive bash scripting, and vector and geometric calculations using MATLAB.

Published a paper with the first authorship: “Huang, CY., Draczkowski, P., Wang, YS. et al. In situ structure and dynamics of an alphacoronavirus spike protein by cryo-ET and cryo-EM. Nat Commun 13, 4877 (2022)”

Master’s Thesis Project: Microscopy Automation at UCL LMCB, London, UK (Sep ’19 – May ’20)

I created a focus-locking system for an open-source microscope from the ground up at Dr Ricardo Henriques’s lab. I utilized CAD software and 3D printing technology to design and prototype customized microscope components. My work involved gaining expertise in optical breadboarding and alignments with Thorlabs tools. I also developed a control system for image acquisition, processing, and control of external devices using Raspberry Pi and programming in Python. After conducting tests and making necessary improvements, I was able to achieve a focal stability of approximately 100 nm.

Theoretical Optics Intern at EMBL, Heidelberg, Germany (Jul – Sep ’19)

Explored techniques to determine the Point Spread Function (PSF) by applying optical theories (such as phase-retrieval method) and discrete Fourier Transform in MATLAB within the lab of Dr Jonas Ries. Designed a user interface for a laser pulse control system using Labview.

Computational Biology Intern at MRC LMB, Cambridge, UK (Jun – Aug ’18)

Worked on cryo-electron tomography reconstruction and sub-tomogram averaging in Dr John Briggs’s lab. I implemented computer vision techniques to develop an algorithm in MATLAB for robust identification of helices in 3D data sets of matrix proteins in influenza viruses, resulting in a contribution to a published paper: “Peukes, J., Xiong, X., Erlendsson, S. et al. The native structure of the assembled matrix protein 1 of influenza A virus. Nature 587, 495–498 (2020)”

Other Projects/ Organized Events

Workshop Lead of the Bioimage Analysis Workshop at Academia Sinica, Taiwan (Jan ’23)

Self-initiated and conducted two one-day workshops on bioimage analysis. The workshops covered both the theoretical and practical aspects of bioimage analysis and included hands-on python exercises. The workshops were attended by over 70 participants from various scientific backgrounds. For more information about the workshops, please visit this GitHub page.

Co-founder and President of UCL SciCon (Jan ’17 – May ’18 & Sep ’19 – Apr ’20)

Founded a society in UCL to encourage two-way conversation about scientific ideas and careers in science, across people in both biological and physical sciences fields and at different career stages.

Led a group to arrange a series of science career and networking events, panel discussions, talks, and lab visits for undergraduate students. Gained experience in taking initiative and putting new ideas into action. Further developed skills in team working and team management.

Scholarships and Awards

Taiwan-Cambridge Scholarship (Sep ’22 - )

European Forum Alpbach, Taiwan Scholarship (Aug ‘20)

UCL Erasmus+ Traineeship Scholarship (Jul ‘19)

Amgen Scholars Programme Cambridge (Jul ‘18)

I was accepted as one of the 20 scholars among 300 applicants from Europe for my internship in Cambridge. Awarded the best poster awards at the end of the programme conference.

UCL ChangeMakers project of the year award (May ‘18)

For the UCL SciCon project

Training Courses Attended

100 Days of Coding in Python, Udemy (Ongoing); Parallel Computing in Python, Udemy (Apr ‘22); Graph Search, Shortest Paths, and Data Structures, Coursera (Jul ’21); Divide and Conquer, Sorting and Searching, and Randomized Algorithms, Coursera (May ’21); Short Course in FPGA chip design and implementation, Taipei IT Training Centre (Mar ’21)