Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis

Yinan Wan*, Jakob El Kholtei, Ignatius Jenie, Mariona Colomer-Rosell, Jialin Liu, Qinghua Zhang, Joaquin Navajas Acedo, Lucia Y Du, Mireia Codina-Tobias, Mengfan Wang, Wei Zheng, Edward Lin, Tzy-Harn Chuang, Oded Mayseless, Ahilya Swah, Susan Mango, Guoqiang Yu, Bogdan Bintu*, Alexandar Schier*, (co-corresponding)

Science, 2026

Single-Cell Reconstruction of Emerging Population Activity in an Entire Developing Circuit.

Yinan Wan*, Ziqiang Wei, L. Looger, Minoru Koyama, S. Druckmann, Philipp J. Keller*, (co-corresponding)

Cell, 2019

The ciliary marginal zone of the zebrafish retina: clonal and time-lapse analysis of a continuously growing tissue

Yinan Wan, Alexandra D. Almeida, S. Rulands, Naima Chalour, Leila Mureşan, Yunmin Wu, B. Simons, Jie He, W. Harris

Development, 2016

Current approaches to fate mapping and lineage tracing using image data.

Steffen Wolf*, Yinan Wan*, K. McDole, (*equal contribution)

Development, 2021

Live Imaging of Zebrafish

Yinan Wan, Philipp J. Keller, Burkhard Höckendorf

Imaging from Cells to Animals In Vivo, 2020

Light-Sheet Microscopy and Its Potential for Understanding Developmental Processes.

Yinan Wan*, K. McDole*, Philipp J. Keller, (*equal contribution)

Annual Review of Cell and Developmental Biology, 2019

High-Fidelity Long-term Whole-embryo Lineage and Fate Reconstruction by Iterative Tracking with Error Correction

Mengfan Wang, Qinghua Zhang, Congchao Wang, Yunfeng Chi, Wei Zheng, Zeyu Mu, Xiangyu Cao, Weizhan Zhang, Boao Yang, Alexander F Schier*, Joaquin Navajas Acedo*, Yinan Wan*, Guoqiang Yu*, (*co-corresponding)

bioRxiv, 2026

Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations

Caroline Malin-Mayor, Peter Hirsch, Leo Guignard, Katie McDole, Yinan Wan, William C Lemon, Dagmar Kainmueller, Philipp J Keller, Stephan Preibisch, Jan Funke

Nature biotechnology, 2023

Nuclear crowding and nonlinear diffusion during interkinetic nuclear migration in the zebrafish retina

Afnan Azizi, A. Herrmann, Yinan Wan, S. J. Buse, Philipp J. Keller, R. Goldstein, W. Harris

eLife, 2020

Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis

Y. Sato, Lennart Hilbert, H. Oda, Yinan Wan, John M. Heddleston, T. Chew, V. Zaburdaev, Philipp J. Keller, T. Lionnet, N. Vastenhouw, H. Kimura

Development, 2019

Adaptive light-sheet microscopy for long-term, high-resolution imaging in living organisms

Loic A. Royer, W. Lemon, R. Chhetri, Yinan Wan, Michael Coleman, E. Myers, Philipp J. Keller

Nature Biotechnology, 2016

Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos.

J. Stegmaier, F. Amat, W. Lemon, K. McDole, Yinan Wan, George Teodoro, R. Mikut, Philipp J. Keller

Developmental Cell, 2016

BlastNeuron for Automated Comparison, Retrieval and Clustering of 3D Neuron Morphologies

Yinan Wan, Fuhui Long, Lei Qu, Hang Xiao, M. Hawrylycz, E. Myers, Hanchuan Peng

Neuroinformatics, 2015

Efficient processing and analysis of large-scale light-sheet microscopy data

F. Amat, Burkhard Höckendorf, Yinan Wan, W. Lemon, K. McDole, Philipp J. Keller

Nature Protocols, 2015

Whole-animal functional and developmental imaging with isotropic spatial resolution

Raghav K Chhetri, Fernando Amat, Yinan Wan, Burkhard Hoeckendorf, William C Lemon, Philipp J Keller

Nature methods, 2015

Efficient extraction of cell shapes and nuclei from 3D light-sheet microscopy images

J. Stegmaier, F. Amat, Masanari Takamiya, A. Bartschat, Jens C. Otte, A. Kobitski, B. Lemon, K. McDole, Yinan Wan, G. Nienhaus, U. Strähle, Philipp J. Keller, R. Mikut

Nature protocols , 2014

Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data

F. Amat, W. Lemon, Daniel P. Mossing, K. McDole, Yinan Wan, K. Branson, E. Myers, Philipp J. Keller

Nature Methods, 2014