Haowen Zhou’s Homepage

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

11/05/2025

I gave an invited talk on Fourier ptychographic microscopy at the International Webinar on Image & Graphics Technologies (Chinese Society for Image & Graphics, online).

08/19/2025

I presented neural-field driven computational microscopy at the Optica Imaging Congress in Seattle.

07/29/2025

Invited talk at Rice University (Houston) titled “Physics-based computational microscopy to advance life science research”.

06/04/2025

ESE Seminar Series (Washington University in St. Louis): “Empowering microscopes with physics-based computation.” Talk page.

04/30/2025

Computer Vision Seminar Series (University of Maryland, College Park): “Synergizing microscopy and computation to advance life science research.”

02/25/2025

Our paper “Single-shot volumetric fluorescence imaging with neural fields” is online at Advanced Photonics. Paper link.

12/03/2024

Awarded the Schmidt Academy for Software Engineering Graduate Research Fellowship supporting Fourier Ptychographic Microscopy software. Schmidt Academy GRA Fellows.

08/06/2024

PNAS publishes “Investigating 3D microbial community dynamics of the rhizosphere using quantitative phase and fluorescence microscopy.” Paper · Science.org news.

05/24/2024

Recipient of the SPIE Optics and Photonics Scholarship. Webpage · PDF · EE News.

03/06/2024

“AI-guided histopathology predicts brain metastasis in lung cancer patients” is featured on the Caltech homepage. News.

03/04/2024

“AI-guided histopathology predicts brain metastasis in lung cancer patients” is now online. Full list here.

02/14/2024

I passed my candidacy exam.

11/21/2023

Launched this personal homepage.

06/30/2021

I joined the Caltech Biophotonics Lab.

View Archive

Selected Publications

Full publication list here.

Digital defocus aberration interference for automated optical microscopy

Haowen Zhou*, Shi Zhao*, Yujie Fan, Zhenyu Dong, Oumeng Zhang, Viviana Gradinaru, Changhuei Yang

arXiv, 2025

BibTex Project Page & Code Data

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).

Analytic Fourier ptychotomography for volumetric refractive index imaging

Zhenyu Dong*, Haowen Zhou*, Ruizhi Cao*, Oumeng Zhang, Shi Zhao, Panlang Lyu, Reinaldo E Alcalde, Changhuei Yang

Nat. Commun. (In Press)

BibTex Project Page & Code Data

We propose Analytic 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.

Single-shot volumetric fluorescence imaging with neural fields

Oumeng Zhang*, Haowen Zhou*, Brandon Y Feng, Elin M Larsson, Reinaldo E Alcalde, Siyuan Yin, Catherine Deng, Changhuei Yang

Advanced Photonics, 2025

BibTex Project Page & Code Data

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.

FPM-INR: Fourier ptychographic microscopy image stack reconstruction using implicit neural representations

Haowen Zhou*, Brandon Y. Feng*, Haiyun Guo, Siyu Lin, Mingshu Liang, Christopher A. Metzler, Changhuei Yang

Optica, 2023

BibTex Project Page & Code Data

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.

AI-guided histopathology predicts brain metastasis in lung cancer patients

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

BibTex Code Data News

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.