I am a PhD candidate in the Department of Electrical Engineering at Caltech, advised by Prof. Changhuei Yang. My current research focuses on:

  • Computational microscopy - empowering imaging techniques with algorithms
  • Synergizing microscopy, computation and artificial intelligence to advance life science research

My aspiration is to become an engineer-scientist who advances scientific discovery through innovative engineering designs.

I am currently on the 2025-2026 job market.

News

08/19/2025 - I presented my work on neural fields for computational microscopy at Optica Imaging Congress, Seattle.
07/29/2025 - I gave an invited talk at Rice University, Houston, on "Physics-based computational microscopy to advance life science research".
06/04/2025 - I delivered an invited talk in ESE Seminar Series at Washington University in St. Louis, titled "Empowering microscopes with physics-based computation" [Talk page]
04/30/2025 - I delivered an invited talk in Computer Vision Seminar Series at University of Maryland, College Park, titled "Synergizing microscopy and computation to advance life science research"
02/25/2025 - Check out our new paper "Single-shot volumetric fluorescence imaging with neural fields" on Advanced Photonics [paper link]
12/03/2024 - I am awarded Schmidt Academy for Software Engineering Graduate Research Fellowship. The support will start on Jan. 2025 for contributions to the algorithm and software development towards computational microscopy, specifically Fourier Ptychographic Microscopy. [Schmidt Academy GRA Fellows]
08/06/2024 - Our new paper titled "Investigating 3D microbial community dynamics of the rhizosphere using quantitative phase and fluorescence microscopy" is online at PNAS. [Science.org News]
05/24/2024 - I am awarded SPIE Optics and Photonics Scholarship. [Webpage] [PDF] [News]
03/06/2024 - The new paper "AI-guided histopathology predicts brain metastasis in lung cancer patients" has been featured on the Caltech homepage. [News]
03/04/2024 - My new paper on "AI-guided histopathology predicts brain metastasis in lung cancer patients" is online today. Check my publication list here!
02/14/2024 - I passed my candidacy exam!
11/21/2023 - My personal homepage is online!
06/30/2021 - I joined Caltech Biophotonics Lab!

Selected Publications

Full publication list here. Clicking paper titles will direct to the preprint or paper page.

Haowen Zhou*, Shi Zhao*, Yujie Fan, Zhenyu Dong, Oumeng Zhang, Viviana Gradinaru, Changhuei Yang
arXiv, 2025
We recently discovered a phenomenon that the digitally summed Fourier spectrum of two images acquired from two-angle illumination exhibits interference-like fringe modulation when the sample is out-of-focus. These digital fringes correlate directly with defocus through a physics-based relation. Based on this principle, we developed an automatic, efficient, and generalizable defocus detection method termed digital defocus aberration interference (DAbI).
DAbI cover image
Zhenyu Dong*, Haowen Zhou*, Ruizhi Cao*, Oumeng Zhang, Shi Zhao, Panlang Lyu, Reinaldo E Alcalde, Changhuei Yang
arXiv, 2025
We propose Fourier Ptychotomography (AFP), a new computational microscopy technique that analytically reconstructs aberration-free, complex-valued 3D RI distributions without iterative optimization or axial scanning. AFP incorporates a new concept named finite sample thickness (FST) prior, thereby simplifying the inverse scattering problem into solving linear equations.
AFP cover image
Oumeng Zhang*, Haowen Zhou*, Brandon Y Feng, Elin M Larsson, Reinaldo E Alcalde, Siyuan Yin, Catherine Deng, Changhuei Yang
Advanced Photonics, 2025
Single-shot volumetric fluorescence (SVF) imaging captures biological processes with high temporal resolution and a large field of view, unlike traditional methods requiring multiple axial plane scans. Existing SVF methods often face limitations due to large, complex point spread functions (PSFs), affecting signal-to-noise ratio, resolution, and field of view. The paper introduces a QuadraPol PSF combined with neural fields, using a compact custom polarizer and a polarization camera to detect fluorescence and encode the 3D scene within a compact PSF without depth ambiguity.
SVF cover image
Haowen Zhou*, Mark Watson*, Cory T. Bernadt, Steven (Siyu) Lin, Chieh-yu Lin, Jon H. Ritter, Alexander Wein, Simon Mahler, Sid Rawal, Ramaswamy Govindan, Changhuei Yang, Richard J. Cote
Journal of Pathology, 2024
Brain metastases can occur in nearly half of patients with early and locally advanced (stage I–III) non-small cell lung cancer (NSCLC). There are no reliable histopathologic or molecular means to identify those who are likely to develop brain metastases. We sought to determine if deep learning could be applied to routine H&E-stained primary tumor tissue sections from stage I–III NSCLC patients to predict the development of brain metastasis.
AI NSCLC cover image
Haowen Zhou*, Brandon Y. Feng*, Haiyun Guo, Siyu Lin, Mingshu Liang, Christopher A. Metzler, Changhuei Yang
Optica, 2023
Fourier ptychographic microscope images the biological samples with high-resolution and large field-of-view simultaneously. However, this microscope faces challenges with long image stack reconstruction time and huge data volumes. We designed physics-based neural signal representations to tackle these challenges and showed potential in facilitating remote diagnosis, digital pathology, and efficient clinical data packaging.
FPM-INR cover image