Leaderboards/Cell Image Analysis Techniques

Cell Image Analysis Techniques

Last updated July 15, 2026

Rising Stars

Fresh ink, massive impact

Researchers

1
Haotian Cui
University Health Network
2
Danielle Maeser
University of Minnesota
3
Vitalii Kleshchevnikov
Wellcome Sanger Institute
4
Amanda Janesick
10X Genomics (United States)
5
Alissa Greenwald
University of Toronto
6
Chenling Xu
Triple Ring Technologies (United States)
7
Kilian Batzner
Software (Germany)
8
Kazumasa Kanemaru
Wellcome/MRC Cambridge Stem Cell Institute
9
Semra Smajić
University of Luxembourg
10
Lucas von Chamier
Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung

Papers

1
scGPT: toward building a foundation model for single-cell multi-omics using generative AI
Nature Methods|2024
1k cit.
2
Integrative spatial analysis reveals a multi-layered organization of glioblastoma
Cell|2024
303 cit.
3
EfficientAD: Accurate Visual Anomaly Detection at Millisecond-Level Latencies
Unknown Journal|2024
265 cit.
4
Towards multimodal foundation models in molecular cell biology
Nature|2025
88 cit.
5
DeepVelo: deep learning extends RNA velocity to multi-lineage systems with cell-specific kinetics
Genome biology|2024
55 cit.
6
Integration of Computational Pipeline to Streamline Efficacious Drug Nomination and Biomarker Discovery in Glioblastoma
Cancers|2024
4 cit.
7
Biomarker Quantification in Breast Cancer using Xenium In Situ
bioRxiv (Cold Spring Harbor Laboratory)|2025
1 cit.
8
Abstract A015: Predicting efficacious drugs and drug-biomarker relationships for targeted glioblastoma treatment
Cancer Research|2024
0 cit.
9
Publication in Cancer Research (2026) [W7148638437]
Cancer Research|2026
0 cit.

Emerging Leaders

Drafting the new consensus

Researchers

1
Marius Pachitariu
Janelia Research Campus
2
Guoji Guo
Zhejiang University
3
Evan Z. Macosko
Broad Institute
4
Tingting Zhao
Tongji University
5
Jeremy Goecks
Moffitt Cancer Center
6
Beth A. Cimini
Broad Institute
7
Allen Goodman
Broad Institute
8
Longqi Liu
Capital Medical University
9
Jonathon Shlens
Google (United States)
10
Guillaume Jacquemet
Åbo Akademi University

Papers

1
Cellpose 2.0: how to train your own model
Nature Methods|2022
1.4k cit.
2
Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson’s disease
Nature Neuroscience|2022
563 cit.
3
Spike sorting with Kilosort4
Nature Methods|2024
390 cit.
4
Cellpose3: one-click image restoration for improved cellular segmentation
Nature Methods|2025
306 cit.
5
Cell transcriptomic atlas of the non-human primate Macaca fascicularis
Nature|2022
214 cit.
6
Early Alzheimer’s disease pathology in human cortex involves transient cell states
Cell|2023
208 cit.
7
The molecular cytoarchitecture of the adult mouse brain
Nature|2023
183 cit.
8
Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis
Developmental Cell|2022
163 cit.
9
High-resolution 3D spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae
Developmental Cell|2022
155 cit.
10
Systematic identification of cell-fate regulatory programs using a single-cell atlas of mouse development
Nature Genetics|2022
103 cit.

Current Senior Leaders

Wrote the book, still writing it

Researchers

1
Kevin W. Eliceiri
University of Wisconsin–Madison
2
Pavel Tomančák
Max Planck Institute of Molecular Cell Biology and Genetics
3
Albert Cardona
University of Cambridge
4
Rahul Satija
New York Genome Center
5
Thomas E. Ferrin
University of California, San Francisco
6
Guido Gerig
New York University
7
Soumya Raychaudhuri
Broad Institute
8
Anne E. Carpenter
Broad Institute
9
Steven A. McCarroll
Broad Institute
10
Garry P. Nolan
Stanford University

Papers

1
Fiji: an open-source platform for biological-image analysis
Nature Methods|2012
70.9k cit.
2
NIH Image to ImageJ: 25 years of image analysis
Nature Methods|2012
65.2k cit.
3
UCSF Chimera—A visualization system for exploratory research and analysis
Journal of Computational Chemistry|2004
47.8k cit.
4
Comprehensive Integration of Single-Cell Data
Cell|2019
16.9k cit.
5
Integrated analysis of multimodal single-cell data
Cell|2021
16k cit.
6
Fast, sensitive and accurate integration of single-cell data with Harmony
Nature Methods|2019
10.5k cit.
7
<scp>UCSF ChimeraX</scp>: Structure visualization for researchers, educators, and developers
Protein Science|2020
10.1k cit.
8
User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability
NeuroImage|2006
9k cit.
9
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
Cell|2015
7.8k cit.
10
Spatial reconstruction of single-cell gene expression data
Nature Biotechnology|2015
7.7k cit.

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