Topic · Cell Image Analysis Techniques
Most cited papers in Cell Image Analysis Techniques
What are the most cited papers in Cell Image Analysis Techniques?
The most cited paper in Cell Image Analysis Techniques is "U-Net: Convolutional Networks for Biomedical Image Segmentation" (Olaf Ronneberger, Philipp F. Fischer, Thomas Brox, 2015), with 92,751 citations. Next come "Fiji: an open-source platform for biological-image analysis" (73,171) and "NIH Image to ImageJ: 25 years of image analysis" (67,169).
Showing 50 of 100 papers. Every paper with more than 1,987 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | U-Net: Convolutional Networks for Biomedical Image Segmentation Olaf Ronneberger, Philipp F. Fischer, Thomas Brox · Lecture notes in computer science | 2015 | 92,751 |
| 2 | Fiji: an open-source platform for biological-image analysis Johannes Schindelin, Ignacio Arganda‐Carreras, Erwin Frise et al. · Nature Methods | 28 Jun 2012 | 73,171 |
| 3 | NIH Image to ImageJ: 25 years of image analysis Caroline A Schneider, Wayne S. Rasband, Kevin W. Eliceiri · Nature Methods | 28 Jun 2012 | 67,169 |
| 4 | phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data Paul J. McMurdie, Susan Holmes · PLoS ONE | 22 Apr 2013 | 23,323 |
| 5 | Comprehensive Integration of Single-Cell Data Tim Stuart, Andrew W. Butler, Paul Hoffman et al. · Cell | Jun 2019 | 17,471 |
| 6 | Visualizing and Understanding Convolutional Networks Matthew D. Zeiler, Rob Fergus · Lecture notes in computer science | 2014 | 15,691 |
| 7 | The Unreasonable Effectiveness of Deep Features as a Perceptual Metric Richard Zhang, Phillip Isola, Alexei A. Efros et al. | Jun 2018 | 13,833 |
| 8 | Fast, sensitive and accurate integration of single-cell data with Harmony Ilya Korsunsky, Nghia Millard, Jean Fan et al. · Nature Methods | 18 Nov 2019 | 11,339 |
| 9 | UCSF ChimeraX : Structure visualization for researchers, educators, and developers Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang et al. · Protein Science | 3 Sep 2020 | 10,674 |
| 10 | nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation Fabian Isensee, Paul F. Jaeger, Simon A. A. Kohl et al. · Nature Methods | 7 Dec 2020 | 9,588 |
| 11 | User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability Paul A. Yushkevich, Joseph Piven, Heather C. Hazlett et al. · NeuroImage | 21 Mar 2006 | 9,244 |
| 12 | QuPath: Open source software for digital pathology image analysis Peter Bankhead, Maurice Bernard Loughrey, José A. Fernández et al. · Scientific Reports | 28 Nov 2017 | 9,140 |
| 13 | Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool Edward Y. Chen, Christopher M. Tan, Yan Kou et al. · BMC Bioinformatics | 15 Apr 2013 | 8,650 |
| 14 | Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets Evan Z. Macosko, Anindita Basu, Rahul Satija et al. · Cell | May 2015 | 8,040 |
| 15 | Unified segmentation John Ashburner, Karl John Friston · NeuroImage | 2 Apr 2005 | 7,633 |
| 16 | SCENIC: single-cell regulatory network inference and clustering Sara Aibar, Carmen Bravo González‐Blas, Thomas Moerman et al. · Nature Methods | 9 Oct 2017 | 7,321 |
| 17 | The sva package for removing batch effects and other unwanted variation in high-throughput experiments Jeffrey T. Leek, William Evan Johnson, Hilary S. Parker et al. · Bioinformatics | 17 Jan 2012 | 6,930 |
| 18 | ImageJ2: ImageJ for the next generation of scientific image data Curtis Rueden, Johannes Schindelin, Mark Hiner et al. · BMC Bioinformatics | 29 Nov 2017 | 6,379 |
| 19 | THE GREEN FLUORESCENT PROTEIN Roger Y. Tsien · Annual Review of Biochemistry | Jun 1998 | 6,213 |
| 20 | Computer Visualization of Three-Dimensional Image Data Using IMOD James R. Kremer, David N. Mastronarde, J. Richard McIntosh · Journal of Structural Biology | 1996 | 6,195 |
| 21 | Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain Brian Avants, Charles L. Epstein, Murray Grossman et al. · Medical Image Analysis | 26 Jun 2007 | 6,189 |
| 22 | Genome-wide atlas of gene expression in the adult mouse brain Ed S. Lein et al. · Nature | 6 Dec 2006 | 6,052 |
| 23 | UCSF ChimeraX: Meeting modern challenges in visualization and analysis Thomas D. Goddard, Conrad C. Huang, Elaine C. Meng et al. · Protein Science | 14 Jul 2017 | 6,046 |
| 24 | Dimensionality reduction for visualizing single-cell data using UMAP Étienne Becht, Leland McInnes, John Healy et al. · Nature Biotechnology | 3 Dec 2018 | 5,903 |
| 25 | Predictive coding in the visual cortex: a functional interpretation of some extra-classical receptive-field effects Rajesh P. N. Rao, Dana H. Ballard · Nature Neuroscience | 1999 | 5,887 |
| 26 | A guided tour into subcellular colocalization analysis in light microscopy Susanne Bolte, Fabrice P. Cordelières · Journal of Microscopy | Dec 2006 | 5,686 |
| 27 | CellProfiler: image analysis software for identifying and quantifying cell phenotypes Anne E. Carpenter, Thouis R. Jones, Michael R. Lamprecht et al. · Genome biology | 31 Oct 2006 | 5,571 |
| 28 | Cytoscape 2.8: new features for data integration and network visualization Michael E. Smoot, Keiichiro Ono, Johannes Ruscheinski et al. · Bioinformatics | 12 Dec 2010 | 5,078 |
| 29 | Thresholding of Statistical Maps in Functional Neuroimaging Using the False Discovery Rate Christopher R. Genovese, Nicole A. Lazar, Thomas E. Nichols · NeuroImage | Apr 2002 | 5,056 |
| 30 | Determining cell type abundance and expression from bulk tissues with digital cytometry Aaron M. Newman, Chloé Beate Steen, Chih Long Liu et al. · Nature Biotechnology | 6 May 2019 | 5,050 |
| 31 | Rapid colorimetric assay for cell growth and survival François Denizot, Rita Lang · Journal of Immunological Methods | May 1986 | 4,918 |
| 32 | xCell: digitally portraying the tissue cellular heterogeneity landscape Dvir Aran, Zicheng Hu, Atul Janardhan Butte · Genome biology | 15 Nov 2017 | 4,825 |
| 33 | On Pixel-Wise Explanations for Non-Linear Classifier Decisions by Layer-Wise Relevance Propagation Sebastian Bach, Alexander Binder, Grégoire Montavon et al. · PLoS ONE | 10 Jul 2015 | 4,700 |
| 34 | Cellpose: a generalist algorithm for cellular segmentation Carsen Stringer, Tim Wang, Michalis Michaelos et al. · Nature Methods | 14 Dec 2020 | 4,662 |
| 35 | 1,500 scientists lift the lid on reproducibility Monya Baker · Nature | 24 May 2016 | 4,397 |
| 36 | Deep tissue two-photon microscopy Fritjof Helmchen, Winfried T. Denk · Nature Methods | 18 Nov 2005 | 4,229 |
| 37 | Snakes, shapes, and gradient vector flow Chenyang Xu, Jerry L. Prince · IEEE Transactions on Image Processing | Mar 1998 | 4,002 |
| 38 | TrackMate: An open and extensible platform for single-particle tracking Jean-Yves Tinévez, Nick Perry, Johannes Schindelin et al. · Methods | 7 Oct 2016 | 3,890 |
| 39 | Evaluation of a tetrazolium-based semiautomated colorimetric assay: assessment of chemosensitivity testing. James Carmichael, William DeGraff, Adi F. Gazdar et al. · PubMed | 15 Feb 1987 | 3,829 |
| 40 | Spatial registration and normalization of images Karl John Friston, John Ashburner, Chris Frith et al. · Human Brain Mapping | 1995 | 3,799 |
| 41 | ilastik: interactive machine learning for (bio)image analysis Stuart Berg, Dominik Kutra, Thorben Kroeger et al. · Nature Methods | 30 Sep 2019 | 3,760 |
| 42 | From molecular to modular cell biology Leland H. Hartwell, J. J. Hopfield, Stanislas Leibler et al. · Nature | 2 Dec 1999 | 3,729 |
| 43 | Network motifs: theory and experimental approaches Uri S. Alon · Nature Reviews Genetics | 18 May 2007 | 3,473 |
| 44 | Adaptive linear step-up procedures that control the false discovery rate Yoav Benjamini, Abba M Krieger, Daniel Yekutieli · Biometrika | Sep 2006 | 3,404 |
| 45 | ROCR: visualizing classifier performance in R Tobias Sing, Oliver Sander, Niko Beerenwinkel et al. · Computer applications in the biosciences | 11 Aug 2005 | 3,374 |
| 46 | VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R Hanbo Chen, Paul Christopher Boutros · BMC Bioinformatics | 26 Jan 2011 | 3,374 |
| 47 | Relations between the statistics of natural images and the response properties of cortical cells David J Field · Journal of the Optical Society of America A | Dec 1987 | 3,302 |
| 48 | Applications of machine learning in drug discovery and development Jessica J. Vamathevan, Dominic A. Clark, Paul Czodrowski et al. · Nature Reviews Drug Discovery | 11 Apr 2019 | 3,274 |
| 49 | Open source clustering software Michiel de Hoon, Seiya Imoto, John P. Nolan et al. · Bioinformatics | 10 Feb 2004 | 3,213 |
| 50 | Imaging Neuronal Subsets in Transgenic Mice Expressing Multiple Spectral Variants of GFP Guoping Feng, Rebecca H. Mellor, Michael B. Bernstein et al. · Neuron | Oct 2000 | 3,168 |
Citations are OpenAlex's own counts, from its 2026-09-23 snapshot, so the ranking can differ from Google Scholar or Web of Science. A paper is listed for a field when OpenAlex files it under one of the field's topics; retracted papers and papers whose citation count cannot be traced to citing works are left out, and a preprint and the article it became are shown once. Release dates are OpenAlex's: where a source gave only a month or a year, that is what is shown. How the lists are chosen.