Donglai Wei
Assistant Professor of Computer Science
Boston College
Office: 245 Beacon St., Rm 528F
Email: donglai.wei [AT]

Github / Google Scholar

I spent memorable postdoc years with Hanspeter Pfister and Jeff Lichtman at Harvard University. I was fortunate to be supervised by William Freeman during my Ph.D. study at MIT CSAIL. I finished my undergraduate in Maths from Brown University (transferred from Tsinghua University), where I was privileged to work under Charles Lawrence, Erik Sudderth, Stuart Geman, and See-Chen Ying.


Our group studies the interplay between natural and artificial intelligence: building computational models for brain image analysis and examining brain mechanisms to guide computer video understanding.
The group is grateful for the support from: NSF-CAREER.


CSCI 3383: Algorithms: F23
CSCI 3343: Computer Vision: F22, F21
CSCI 3397: Biomedical Image Analysis. S22, S23, S24

Office Hours

Now Looking For: postdocs, visiting scholars and research interns.

Lab members

Software Engineer: Mansour Alawi
Undergrad: Jason Adhinarta Joshua Gorniak Michael Lin Steven Roche


Master: Zengyu Yang

Publications [Dataset, Natrual Intelligence]


S3-TTA: Scale-Style Selection for Test-Time Augmentation in Biomedical Image Segmentation

Kangxian Xie, Siyu Huang, Sebastian Andres Cajas Ordonez, Hanspeter Pfister, Donglai Wei
ISBI 2024

LLCP: Learning Latent Causal Processes for Reasoning-based Video Question Answer

Guangyi Chen, Yuke Li, Xiao Liu, Zijian Li, Eman Al Suradi, Donglai Wei, Kun Zhang
ICLR 2024


CLIPTrans: Transferring Visual Knowledge with Pre-trained Models for Multimodal Machine Translation

Devaansh Gupta, Siddhant Kharbanda, Jiawei Zhou, Wanhua Li, Hanspeter Pfister, Donglai Wei
ICCV 2023
[Website] [Code]

VizAbility: Multimodal Accessible Data Visualization with Keyboard Navigation and Conversational Interaction

Joshua Gorniak, Jake Ottiger, Donglai Wei, Nam Wook Kim
UIST 2023

Domain-Scalable Unpaired Image Translation via Latent Space Anchoring

Siyu Huang, Jie An, Donglai Wei, Zudi Lin, Jiebo Luo, Hanspeter Pfister
TPAMI 2023

QuantArt: Quantizing Image Style Transfer Towards High Visual Fidelity

Siyu Huang, Jie An, Donglai Wei, Jiebo Luo, Hanspeter Pfister
CVPR 2023

Why is the winner the best?

Matthias Eisenmann, ..., Donglai Wei, ..., Lena Maier-hein
CVPR 2023

Current Progress and Challenges in Large-scale 3D Mitochondria Instance Segmentation

Daniel Franco-Barranco, Zudi Lin, Won-Dong Jang, Xueying Wang, Qijia Shen, Wenjie Yin, Yutian Fan, Mingxing Li, Chang Chen, Zhiwei Xiong, Rui Xin, Hao Liu, Huai Chen, Zhili Li, Jie Zhao, Xuejin Chen, Constantin Pape, Ryan Conrad, Luke Nightingale, Joost de Folter, Martin Jones, Yanling Liu, Dorsa Ziaei, Stephan Huschauer, Ignacio Arganda-Carreras, Hanspeter Pfister, Donglai Wei
TMI 2023
[Website (code/data)]

RibSeg v2: A Large-scale Benchmark for Rib Labeling and Anatomical Centerline Extraction

Liang Jin, Shixuan Gu, Donglai Wei, Jason Adhinarta, Kaiming Kuang, Yongjie Zhang, Hanspeter Pfister, Bingbing Ni, Jiancheng Yang, Ming Li
TMI 2023
[Website (code/data)]

Structure-Preserving Instance Segmentation via Skeleton-Aware Distance Transform

Zudi Lin, Donglai Wei, Aarush Gupta, Xingyu Liu, Deqing Sun, Hanspeter Pfister
MICCAI 2023 [Oral]
[Code][Website (coming soon)]

High-Throughput Microscopy Image Deblurring with Graph Reasoning Attention Network

Yulun Zhang, Donglai Wei, Richard Schalek, Yuelong Wu, Stephen Turney, Jeff Lichtman, Hanspeter Pfister, Yun Fu
ISBI 2023 (later: Microscopy and Microanalysis 2023)

Learning Vector Quantized Shape Code for Amodal Blastomere Instance Segmentation

Won-Dong Jang, Donglai Wei, Xingxuan Zhang, Brian Leahy, Helen Yang, James Tompkin, Dalit Ben-Yosef, Daniel Needleman, Hanspeter Pfister
ISBI 2023

Multi-task Curriculum Learning for Partially Labeled Data

Won-Dong Jang, Stanislav Lukyanenko, Donglai Wei, Jiancheng Yang, Brian Leahy, Helen Yang, Dalit Ben-Yosef, Daniel Needleman, Hanspeter Pfister
ISBI 2023 [Oral]

3D Domain Adaptive Instance Segmentation Via Cyclic Segmentation GANs

Leander Lauenburg, Zudi Lin, Ruihan Zhang, Márcia dos Santos, Siyu Huang, Ignacio Arganda-Carreras, Edward Boyden, Hanspeter Pfister, Donglai Wei
JBHI 2023
[Website (code)][Dataset]

BlastAssist: A Deep Learning Pipeline to Measure Interpretable Features of Human Embryos

Helen Yang, Brian Leahy, Won-Dong Jang, Donglai Wei, Yael Kalma, Roni Rahav, Ariella Carmon, Rotem Kopel, Foad Azem, Marta Venturas, Colm Kelleher, Liz Cam, Hanspeter Pfister, Daniel Needleman, Dalit Ben-Yosef
Human Reproduction 2023

Vimo: Visual Analysis of Neuronal Connectivity Motifs

Jakob Troidl, Simon Warchol, Jinhan Choi, Jordan Matelsky, Nagaraju Dhanyasi, Xueying Wang, Brock Wester, Donglai Wei, Jeff Lichtman, Hanspeter Pfister, Johanna Beyer
VIS 2023
[Website (code)]

Dense 4D nanoscale reconstruction of living brain tissue

Philipp Velicky, Eder Miguel, Julia M. Michalska, Donglai Wei, Zudi Lin, Jake F. Watson, Jakob Troidl, Johanna Beyer, Yoav Ben-Simon, Christoph Sommer, Wiebke Jahr, Alban Cenameri, Johannes Broichhagen, Seth G. N. Grant, Peter Jonas, Gaia Novarino, Hanspeter Pfister, Bernd Bickel, Johann G. Danzl
Nature Methods 2023

Immersion fixation and staining of multi-cubic millimeter volumes for electron microscopy-based connectomics of human brain biopsies

Neha Karlupia, Richard Schalek, Yuelong Wu, Yaron Meirovitch, Donglai Wei, Alexander Charney, Brian Kopell, Jeff Lichtman
Biological Psychiatry 2023

Multiplexed Volumetric CLEM enabled by antibody derivatives provides new insights into the cytology of the mouse cerebellar cortex

Xiaomeng Han, Xiaotang Lu, Peter Li, Shuohong Wang, Richard Schalek, Yaron Meirovitch, Zudi Lin, Jason Adhinarta, Daniel Berger, Yuelong Wu, Tao Fang, Elif Sevde Meral, Shadnan Asraf, Hidde Ploegh, Hanspeter Pfister, Donglai Wei, Viren Jain, James Trimmer, Jeff Lichtman
bioarxiv 2023

A large-scale volumetric correlated light and electron microscopy study localizes Alzheimer's disease-related molecules in the hippocampus

Xiaomeng Han, Shuohong Wang, Morgan Sanchez, Sneha Aggarwal, Richard Schalek, Yaron Meirovitch, Zudi Lin, Yuelong Wu, Fatima Aly, Sylvie Bay, Benoît Delatour, Pierre Lafaye, Hanspeter Pfister, Donglai Wei, Hidde Ploegh, Jeff Lichtman
bioarxiv 2023


YouMVOS: An Actor-centric Multi-shot Video Object Segmentation Dataset

Donglai Wei, Siddhant Kharbanda, Sarthak Arora, Roshan Roy, Nishant Jain, Akash Palrecha, Tanav Shah, Shray Mathur, Ritik Mathur, Abhijay Kemka, Anirudh Chakravarthy, Zudi Lin, Won-Dong Jang, Yansong Tang, Song Bai, James Tompkin, Philip H.S. Torr, Hanspeter Pfister
CVPR 2022
[Website (code)]

Texture-based Error Analysis for Image Super-Resolution

Salma Abdel Magid, Zudi Lin, Donglai Wei, Yulun Zhang, Jinjin Gu, Hanspeter Pfister
CVPR 2022
[Website (code)]

Scalable Biologically-Aware Skeleton Generation for Connectomic Volumes

Brian Matejek, Tim Franzmeyer, Donglai Wei, Xueying Wang, Jinglin Zhao, Kálmán Palágyi, Jeff W. Lichtman, Hanspeter Pfister
TMI 2022
[Website (code/data)]

UnMICST: Deep Learning with Real Augmentation for Robust Segmentation of Highly Multiplexed Images of Human Tissues

Clarence Yapp, Edward Novikov, Won-Dong Jang, Yu-An Chen, Marcelo Cicconet, Zoltan Maliga, Connor A. Jacobson, Donglai Wei, Sandro Santagata, Hanspeter Pfister, Peter K. Sorger
Communications Biology 2022

Edge-Colored Directed Subgraph Enumeration on the Connectome

Brian Matejek, Donglai Wei, Tianyi Chen, Charalampos Tsourakakis, Michael Mitzenmacher, Hanspeter Pfister
Scientific Reports 2022
[Website (code/data)]

MedMNIST v2: A Large-Scale Lightweight Benchmark for 2D and 3D Biomedical Image Classification

Jiancheng Yang, Rui Shi, Donglai Wei, Zequan Liu, Lin Zhao, Bilian Ke, Hanspeter Pfister, and Bingbing Ni
Scientific Data 2022
[Website (code/data)]


Learning to Generate Realistic Noisy Images via Pixel-level Noise-aware Adversarial Training

Yuanhao Cai, Xiaowan Hu, Haoqian Wang, Yulun Zhang, Hanspeter Pfister, Donglai Wei
NeurIPS 2021
[Website (code)]

Dynamic High-Pass Filtering and Multi-Spectral Attention for Image Super-Resolution

Salma Abdel Magid, Yulun Zhang, Donglai Wei, Won-Dong Jang, Zudi Lin, Yun Fu, Hanspeter Pfister
ICCV 2021
[Website (code)]

Context Reasoning Attention Network for Image Super-Resolution

Yulun Zhang, Donglai Wei, Can Qin, Huan Wang, Hanspeter Pfister, Yun Fu
ICCV 2021

AxonEM Dataset: 3D Axon Instance Segmentation of Brain Cortical Regions

Donglai Wei*, Kisuk Lee*, Hanyu Li, Ran Lu, J. Alexander Bae, Zequan Liu, Lifu Zhang, Márcia dos Santos, Zudi Lin, Thomas Uram, Xueying Wang, Ignacio Arganda-Carreras, Brian Matejek, Narayanan Kasthuri, Jeff Lichtman, Hanspeter Pfister
[Website (code/data)][Challenge]

NucMM Dataset: 3D Neuronal Nuclei Instance Segmentation at Sub-Cubic Millimeter Scale

Zudi Lin*, Donglai Wei*, Mariela Petkova, Yuelong Wu, Zergham Ahmed, Krishna Swaroop K, Silin Zou, Nils Wendt, Jonathan Boulanger-Weill, Xueying Wang, Nagaraju Dhanyasi, Ignacio Arganda-Carreras, Florian Engert, Jeff Lichtman, Hanspeter Pfister
MICCAI 2021 (Student Travel Award)
[Website (code/data)][Challenge]

Developmental Stage Classification of Embryos Using Two-Stream Neural Network with Linear-Chain Conditional Random Field

Stanislav Lukyanenko, Won-Dong Jang, Donglai Wei, Robbert Struyven, Yoon Kim, Brian Leahy, Helen Yang, Alexander Rush, Dalit Ben-Yosef, Daniel Needleman, Hanspeter Pfister
MICCAI 2021 (nominated but ineligible for Student Travel Award)
[Website (code)]

RibSeg Dataset and Strong Point Cloud Baselines for Rib Segmentation from CT Scans

Jiancheng Yang, Shixuan Gu, Bingbing Ni, Donglai Wei, Hanspeter Pfister
[Website (code/data)]

Consistent Recurrent Neural Networks for 3D Neuron Segmentation

Felix Gonda, Donglai Wei, Hanspeter Pfister
ISBI 2021

The Wood Image Analysis and Dataset (WIAD): open-access visual analysis tools to advance the ecological data revolution

Tim Rademacher, Bijan Seyednasrollah, David Basler, Jian Cheng, Tessa Mandra, Elise Miller, Zudi Lin, David A Orwig, Neil Pederson, Hanspeter Pfister, Andrew D Richardson, Donglai Wei, Li Yao
Methods in Ecology and Evolution 2021

A Connectomic Study of A Petascale Fragment of Human Cerebral Cortex

Alexander Shapson-Coe, Michał Januszewski, Daniel Berger, Art Pope, Yuelong Wu, Tim Blakely, Richard Schalek, Peter Li, Shuohong Wang, Jeremy Maitin-Shepard, Neha Karlupia, Sven Dorkenwald, Evelina Sjostedt, Laramie Leavitt, Dongil Lee, Luke Bailey, Angerica Fitzmaurice, Rohin Kar, Benjamin Field, Hank Wu, Julian Wagner-Carena, David Aley, Joanna Lau, Zudi Lin, Donglai Wei, Hanspeter Pfister, Adi Peleg, Viren Jain, Jeff W. Lichtman
biorxiv 2021
[Google AI blog][Gallery]


Super-BPD: Super Boundary-to-Pixel Direction for Fast Image Segmentation

Jianqiang Wan, Yang Liu, Donglai Wei, Xiang Bai, Yongchao Xu
CVPR 2020

A Topological Nomenclature for 3D Shape Analysis in Connectomics

Abhimanyu Talwar, Zudi Lin, Donglai Wei, Yuesong Wu, Bowen Zheng, Jinglin Zhao, Won-Don Jang, Xueying Wang, Jeff Lichtman, Hanspeter Pfister
CVPR 2020 Workshop: Computer Vision for Microscopy Image Analysis

Two-Stream Active Query Suggestion for Large-Scale Object Detection in Connectomics

Zudi Lin, Donglai Wei, Won-Dong Jang, Siyan Zhou, Xupeng Chen, Xueying Wang, Richard L. Schalek, Daniel R. Berger, Brian Matejek, Lee D. Kamentsky, Adi Peleg, Daniel Haehn, Thouis R. Jones, Toufiq Parag, Jeff Lichtman, Hanspeter Pfister
ECCV 2020
[Website (code/data)][Supp]

MitoEM Dataset: Large-scale 3D Mitochondria Instance Segmentation from EM Images

Donglai Wei, Zudi Lin, Daniel Franco-Barranco, Nils Wendt, Xingyu Liu, Wenjie Yin, Xin Huang, Aarush Gupta, Won-Dong Jang, Xueying Wang, Ignacio Arganda-Carreras, Jeff Lichtman, Hanspeter Pfister
[Website (code/data)][Challenge]

Automated Measurement of Key Morphological Features of Human Embryos for IVF

Brian Leahy*, Won-Dong Jang*, Helen Yang*, Robbert Struyven, Donglai Wei, Zhe Sun, Kylie R. Lee, Charlotte Royston, Liz Cam, Yael Kalma, Foad Azem, Dalit Ben-Yosef, Hanspeter Pfister, Daniel Needleman
[Website (code)]

Channel Embedding for Informative Protein Identification from Highly Multiplexed Images

Salma A. Magid, Won-Dong Jang, Denis Schapiro, Donglai Wei, James Tompkin, Peter Sorger, Hanspeter Pfister
[Website (code)]

Pulse-driven robot: Motion via Solitary Waves

Bolei Deng, Liyuan Chen, Donglai Wei, Vincent Tournat, Katia Bertoldi
Science Advances 2020


Video Enhancement with Task-Oriented Flow

Tianfan Xue, Baian Chen, Jiajun Wu, Donglai Wei, William T. Freeman
IJCV 2019

Synapse-Aware Skeleton Generation for Neural Circuits

Brian Matejek, Donglai Wei, Xueying Wang, Jinglin Zhao, Kálmán Palágyi, Hanspeter Pfister
[Website (code)][Video]

Biologically-Constrained Graphs for Global Connectomics Reconstruction

Brian Matejek, Daniel Haehn, Haidong Zhu, Donglai Wei, Toufiq Parag, Hanspeter Pfister
CVPR 2019


Learning and Using the Arrow of Time

Donglai Wei, Joseph Lim, Andrew Zisserman, Wlliam T. Freeman
CVPR 2018
[Website (code/data)][Extension]

Parallel Separable 3D Convolution for Video and Volumetric Data Understanding

Felix Gonda, Donglai Wei, Toufiq Parag, Hanspeter Pfister
BMVC 2018

Detecting Synapse Location and Connectivity by Signed Proximity Estimation and Pruning with Deep Nets

Toufiq Parag, Daniel Berger, Lee Kamentsky, Benedikt Staffler, Donglai Wei, Moritz Helmstaedter, Jeff W. Lichtman, Hanspeter Pfister
ECCV 2018 Workshop: Bioimage Computing

Before 2018

Motion Microscopy for Visualizing and Quantifying Small Motions

Neal Wadhwa, Justin G. Chen, Jonathan B. Sellon, Donglai Wei, Michael Rubinstein, Roozbeh Ghaffari, Dennis M. Freeman, Oral Büyüköztürk, Pai Wang, Sijie Sun, Sung Hoon Kang, Katia Bertoldi, Fredo Durand, William T. Freeman
PNAS 2017
[Website (code)]

Mining Visual Evolution in 21 Years of Web Design

Ali Jahanian, Philip Isola, Donglai Wei
CHI Extended Abstracts 2017

Deviation Magnification: Revealing Departures from Ideal Geometries

Neal Wadhwa, Tali Dekel, Donglai Wei, Fredo Durand, William T. Freeman
SIGGRAPH Asia 2015

Understanding Intra-Class Knowledge inside CNN

Donglai Wei, Bolei Zhou, Antonio Torralba, William T. Freeman
arxiv 2015
[Website (code)][]

Seeing the Arrow of Time

Lindsey Pickup, Zheng Pan, Donglai Wei, Yichang Shih, Changshui Zhang, Andrew Zisserman, Bernhard Schölkopf, William T. Freeman
CVPR 2014

A Data-driven Regularization Model for Stereo and Flow

Donglai Wei, Ce Liu, William T. Freeman
3DV 2014 [Oral]

Video Representation Using Temporal Superpixels

Jason Chang, Donglai Wei, John Fisher III
CVPR 2013

Learning Deformations with Parallel Transport

Donglai Wei, Dahua Lin, John Fisher III
ECCV 2012

RNAG: A New Gibbs Sampler for Predicting RNA Secondary Structure for Unaligned Sequences

Donglai Wei, Lauren Alpert and Charles Lawrence
Bioinformatics 2011
[Website (code)]


MedAGI: Foundation Models for General Medical AI

Won-Ki Jeong, Hyunwoo Kim, Yiqing Shen, Zhongying Deng, Edward Choi, Junjun He, Hoon Cho, Donglai Wei, Jin Ye, Jing Ke
MICCAI Workshop 2023

RnR-ExM: Robust Non-rigid Registration Challenge for Expansion Microscopy Volumes

Emma Besier, Ruihan Zhang, Yosuke Bando, Yves Quéméner, Chaitanya Kapoor, Mansour Alawi, Malte Hoffmann, Adrian Dalca, Adrià Casamitjana, Ignacio Arganda-Carreras, Ed Boyden, Hanspeter Pfister, Donglai Wei
ISBI Challenge 2023

[Computer Vision News]

An Out-of-Domain Synapse Detection Challenge for Microwasp Brain Connectomes

Jingpeng Wu, Yicong Li, Kazunori Shinomiya, Pat Gunn, Alexey Polilov, Hanspeter Pfister, Dmitri Chklovskii, Donglai Wei
ISBI Challenge 2023

[Computer Vision News]

XPRESS: Xray Projectomic Reconstruction (Extracting Segmentation with Skeletons)

Mukul Narwani, Mark Larson, Tri Nguyen, Yicong Li, Hanspeter Pfister, Donglai Wei, Nir Shavit, Lu Mi, Alexandra Pacureanu, Wei-Chung Lee, Aaron Kuan
ISBI Challenge 2023

Neuroimage Informatics at the Microscale and Mesoscale

Jingpeng Wu, Donglai Wei, Anan Li, Linqing Feng, Shang Mu
Research Topics @ Frontiers in Neuroinformatics

MitoEM Challenge: Large-scale 3D Mitochondria Instance Segmentation

Donglai Wei, Zudi Lin, Daniel Franco-Barranco, Wenjie Yin, Won-Dong Jang, Xueying Wang, Ignacio Arganda-Carreras, Jeff Lichtman, Hanspeter Pfister
ISBI Challenge 2021

RibFrac Challenge: Rib Fracture Detection and Classification

Jiancheng Yang, Xiaoyang Huang, Kaiming Kuang, Jiajun Chen, Liang Jin, Donglai Wei, Ming Li, Bingbing Ni
MICCAI Challenge 2020


Short Bio

daqing guangzhou Born and grown up in China
tsinghua brown mit mit Gradually became lost, ignorant, but arrogant
Jesus Born again