Fluorescence Microscopy

Latest papers

20 papers4 papers in the last four weeks, with none the four weeks before. 0.0% of all new papers.

MicroCLIP: Connecting Text and Microscopy Images via Contrastive Language--Image Pretraining
Oct 13, 2026Yanran Ruan, Zhixiang Wei, Shiyao Hong +5Fluorescence Microscopy Microscopy Image Analysis
University of Science and Technology of China
Protein Crystallization Segmentation and Classification Using Subordinate Color Channel in Fluorescence Microscopy Images
Oct 11, 2026Truong X. Tran, Marc L. Pusey, Ramazan S. AygunFluorescence Microscopy Microscopy Image Analysis
Data Media Lab, Computer Science Department, The University of Alabama in Huntsville, USA. · XpressGenes, Inc, Huntsville, Alabama, USA. · Chemistry Departement, The University of Alabama in Huntsville, USA.
Detection of extremely rare dead cells in fluorescence microscopy images
Oct 9, 2026Prateek Verma, Benjamin Butter, Jian Zhang +1Microscopy Image Analysis Fluorescence Microscopy
Department of Electrical Engineering and Computer Science University of Arkansas, Fayetteville, Arkansas, USA · Department of Biomedical Engineering University of Arkansas, Fayetteville, Arkansas, USA
FACET: Factorized Asymmetric Conditioning for Efficient Transport in High-Fidelity Fluorescence Microscopy Synthesis
Oct 4, 2026Sazan Mahbub, Caleb N. Ellington, Eric P. XingConditional Image Generation Diffusion-Based Image Generation
Carnegie Mellon University · GenBio AI · Mohamed bin Zayed University of AI
BMND: Direct Poisson Denoising by N-Dimensional Block Matching and Collaborative Filtering
Sep 28, 2026Christof Duhme, Lars Schiefelbein, Florian Büther +1Fluorescence Microscopy Image Denoising
University of Münster
NeuroRefiner: Morphology-Aware Multi-Agent Refinement for 3D Fluorescence Microscopy Neuron Segmentation
Aug 10, 2026Haiyang Yan, Jinyue Guo, Yanchao Zhang +6Topology-Preserving Image Segmentation Fluorescence Microscopy
State Key Laboratory of Brain Cognition and Brain-inspired Intelligence Technology, Institute of Automation, Chinese Academy of Sciences · School of Future Technology, University of Chinese Academy of Sciences · School of Artificial Intelligence, University of Chinese Academy of Sciences +1
Physics-Informed Deep Learning Model for Cross-Modality Super-Resolution in Fluorescence Microscopy
Jul 23, 2026Mohammad Soltaninezhad, Elena Corbetta, Francisco Paez Larios +4Image-to-Image Translation Physics-Informed ML
Department “Photonic Data Science”, Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Member of the Leibniz Center for Photonics in Infection Research (LPI), Jena, Germany · Work group “Photonic Data Science”, Institute of Physical Chemistry (IPC) and Abbe Center of Photonics (ACP), Friedrich Schiller University Jena, Member of the Leibniz Center for Photonics in Infection Research (LPI), Jena, Germany · Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany +3
SWITi: Quantifying and Reducing Tiling Artifacts with Sliding Window Inner Tiling
Jul 21, 2026Federico Carrara, Aman Kukde, Melisande Croft +2Image Reconstruction Fluorescence Microscopy
Fondazione Human Technopole, Milan, Italy · Università Campus Bio-Medico, Rome, Italy
SVC-Probe: A Framework for Evaluating Perturbation Generalization in Spatial Foundation-Model Embeddings
Jun 26, 2026Jake Y. Chen, Huu Phong Nguyen, Fuad Al Abir +1Single-Cell Perturbation Modeling Fluorescence Microscopy
Department of Biomedical Informatics and Data Science, University of Alabama at Birmingham, Birmingham, AL, USA. · System Pharmacology and AI Research Center, University of Alabama at Birmingham, Birmingham, AL, USA.
A Zero-Shot Deep Image Prior Framework for Denoising and Deconvolution in Fluorescence Microscopy
Jun 26, 2026Xiangyu Qian, Jing Liu, Yunqing Tang +2Deep Image Prior Physics-Guided Image Restoration
Wenzhou Key Laboratory of Biomedical Imaging, Zhejiang Key Laboratory of Soft Matter Biomedical Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China · Postgraduate Training Base Alliance of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
3D Masked Autoencoders are Robust Learners of Volumetric and Multimodal Cellular Representations for Microscopy
Jun 22, 2026Amirhossein Kardoost, Lion Gleiter, Tingying Peng +1Cross-Modal Representation Learning Masked Autoencoders
Institute of AI for Health & Helmholtz AI, Computational Health Center, Helmholtz Munich – German Research Center for Environmental Health, Neuherberg, Germany · Munich Center for Machine Learning (MCML), Munich, Germany · Department of Medicine III, Ludwig-Maximilian-University Hospital, Munich, Germany +2
Single-Channel Tissue Segmentation via Cross-Modal Distillation from Foundation Models
May 30, 2026Sakib Mohammad, Jarin Ritu, Md Sakhawat HossainCross-Modal Knowledge Distillation Fluorescence Microscopy
Department of Engineering Technology Fairmont State University Fairmont, WV, USA · Department of Electrical and Computer Engineering Texas A&M University College Station, TX, USA · Department of Mechanical Engineering Auburn University Auburn, AL, USA
A Multimodal 3D Foundation Model for Light Sheet Fluorescence Microscopy Enables Few-Shot Segmentation, Classification, and Deblurring
May 25, 2026Adina Scheinfeld, Haotan Zhang, Shang Mu +53D Semantic Segmentation Microscopy Image Analysis
Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY, USA · Department of Radiology, Weill Cornell Medicine, New York, NY, USA · Helen and Robert Appel Alzheimers Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA +4
Bayesian In Vivo Tracking of Synapses using Joint Poisson Deconvolution and Diffeomorphic Registration
May 13, 2026Shashwat Kumar, Dominic M. Padova, Binish Narang +6Bayesian Inverse Problems Longitudinal Medical Image Analysis
Department of Biomedical Engineering, Johns Hopkins University · Department of Neuroscience, Johns Hopkins University · Kavli Neuroscience Discovery Institute, Johns Hopkins University +2
MTCurv: Deep learning for direct microtubule curvature mapping in noisy fluorescence microscopy images
Apr 29, 2026Achraf Ait Laydi, Sidi Mohamed Sid'El Moctar, Yousef El Mourabit +1Fluorescence Microscopy Convolutional Neural Networks
TIAD Laboratory, Sciences and Technology Faculty, Sultan Moulay Slimane Univ., Beni Mellal, Morocco. · CNRS, Univ. Rennes, IGDR (Institut de Génétique et Développement de Rennes), UMR6290, 35000 Rennes, France
SIMPLER: H&E-Informed Representation Learning for Structured Illumination Microscopy
Apr 11, 2026Abu Zahid Bin Aziz, Syed Fahim Ahmed, Gnanesh Rasineni +8Medical Image Representation Learning Microscopy Image Analysis
Kahlert School of Computing, University of Utah, Salt Lake City, UT 84112, USA · Scientific Computing & Imaging Institute, University of Utah, Salt Lake City, UT 84112, USA · Instapath Inc., Houston, TX 77021 +1
λSplit: Self-Supervised Content-Aware Spectral Unmixing for Fluorescence Microscopy
Mar 24, 2026Federico Carrara, Talley Lambert, Mehdi Seifi +1Spectral Unmixing Microscopy Image Analysis
Fondazione Human Technopole, Milan, Italy · Università Campus Bio-Medico, Rome, Italy · Harvard Medical School, Boston, MA, USA
Ca2+ transient detection and segmentation with the Astronomically motivated algorithm for Background Estimation And Transient Segmentation (Astro-BEATS)
Mar 19, 2026Bolin Fan, Anthony Bilodeau, Frederic Beaupre +4Microscopy Image Analysis Image Segmentation
Dunlap Institute for Astronomy and Astrophysics, University of Toronto, Toronto, Canada · David A. Dunlap Department for Astronomy and Astrophysics, University of Toronto, Toronto, Canada · CERVO Brain Research Center, Québec, Canada +4
Segmentation-before-Staining Improves Structural Fidelity in Virtual IHC-to-Multiplex IF Translation
Mar 17, 2026Junhyeok Lee, Han Jang, Heeseong Eum +2Virtual Staining Medical Image Synthesis
Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul, Republic of Korea · Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea · Department of Biomedical Sciences, Seoul National University, Seoul, Republic of Korea +3
FluoCLIP: Stain-Aware Focus Quality Assessment in Fluorescence Microscopy
Feb 27, 2026Hyejin Park, Jiwon Yoon, Sumin Park +5Fluorescence Microscopy Microscopy Image Analysis
Division of AI and Software, Ewha Womans University, South Korea · Analytical Solution Team, Daesang Corporation, South Korea · Bioimaging Data Curation Center (BDCC), Department of Life Science, Ewha Womans University, South Korea

Oct 13, 2026J/K move · Enter open · S save

MicroCLIP: Connecting Text and Microscopy Images via Contrastive Language--Image Pretraining

Yanran Ruan, Zhixiang Wei, Shiyao Hong, Xiaoxiao Ma+4

University of Science and Technology of China

Fluorescence Microscopy Microscopy Image Analysis Vision-Language Alignment Zero-Shot Image Classification Multimodal Contrastive Learning

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Understanding fluorescence microscopy images is fundamental to automating biological research. However, existing methods typically learn predefined concepts from closed-set data, limiting transfer across tasks and biological contexts. In this work, we introduce MicroCLIP, a vision-language model that learns generalizable cellular and subcellular representations from natural language supervision for open-set image classification and retrieval. To pretrain MicroCLIP, we construct MicroPool-2M, a dataset of approximately 2.5 million fluorescence microscopy image-text pairs spanning diverse cellular structures, cell lines, and imaging conditions. Aligning microscopy images with biological concepts in natural language is challenging because most images lack descriptive captions and biological knowledge annotations. We therefore progressively establish image-text associations at three levels to provide MicroCLIP with richer semantic supervision: (1) category-level alignment links images to standardized labels defined by subcellular structure-cell-line combinations; (2) knowledge-level alignment incorporates biological priors derived from these labels to capture relationships across species and cell types; and (3) detail-level alignment uses a multimodal large language model to recaption and verify image-text pairs at scale, emphasizing fine-grained visual characteristics. Extensive experiments demonstrate that MicroCLIP achieves leading performance in zero-shot classification and text-image retrieval on microscopy images. It retrieves images with specific cellular characteristics from thousands of candidates and generalizes to unseen biological concepts without additional supervision. These results highlight MicroCLIP's potential as a foundation model for fluorescence microscopy.