Image Processing, Quantitative Microscopy, Colocalisation
General
2017
- external pageAnalysis of live cell images: Methods, tools and opportunities. Nketia TA, Sailem H, Rohde G, Machiraju R, Rittscher Jcall_made
- external pageSingle Particle Tracking: From Theory to Biophysical Applications Shen H, Tauzin LJ, Baiyasi R, Wang W, Moringo N, Shuang B, Landes CFcall_made
- external pageA BaSiC tool for background and shading correction of optical microscopy images Peng T, Thorn K, Schroeder T, Wang L, Theis FJ, Marr C, Navab Ncall_made
2016
2013
- external pagePost-processing for statistical image analysis in light microscopy. Cardullo RA, Hinchcliffe EH.call_made
- external pageQuantitative analysis of digital microscope images. Wolf DE, Samarasekera C, Swedlow JR.call_made
- external page65,000 shades of grey: use of digital image files in light microscopy. Shaw SL, Hinchcliffe EH.call_made
2012
- external pageBiological imaging software tools. Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurman N, Swedlow JR, Tomancak P, Carpenter AE.call_made
- external pageOpen source tools for fluorescent imaging. Hamilton NA.call_made
- external pageSoftware tools, data structures, and interfaces for microscope imaging. Stuurman N, Swedlow JR.call_made
2009
- external pageAccuracy and precision in quantitative fluorescence microscopy. Waters JC.call_made
- external pageQuantification and its applications in fluorescent microscopy imaging. Hamilton N.call_made
2007
2006
- external pageSeeing is believing? A beginners’ guide to practical pitfalls in image acquisition North, Acall_made
- external pageCellProfiler: image analysis software for identifying and quantifying cell phenotypes. Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DMcall_made
2000
1995
Colocalization
2019
2015
2014
2013
- external pageA novel method for quantified, superresolved, three-dimensional colocalisation of isotropic, fluorescent particles. Obara B1, Jabeen A, Fernandez N, Laissue PP.call_made
- external pageColocalization Analysis in Fluorescence Microscopy. Jeremy Adler and Ingela Parmrydcall_made
- external pageColocalisation Workshop Imaging Core Facility Biozentrum Basel. Ferrand A.call_made
- external pageA novel method for quantified, superresolved, three-dimensional colocalisation of isotropic, fluorescent particles. Obara B, Jabeen A, Fernandez N, Laissue PP.call_made
- external pageColocalization analysis in fluorescence microscopy. Adler J, Parmryd I.call_made
- external pageNew image colocalization coefficient for fluorescence microscopy to quantify (bio-)molecular interactions. Herce HD, Casas-Delucchi CS, Cardoso MC.call_made
2012
2011
2010
- external pageBeyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. Jo A Helmuth, Grégory Paul, and Ivo F Sbalzarinicall_made
- external pageQuantifying Colocalization by Correlation: The Pearson Correlation Coefficient is Superior to the Mander’s Overlap Coefficient Jeremy Adler, Ingela Parmrydcall_made
- external pageQuantifying Colocalization: Thresholding, Void Voxels and the Hcoef Jeremy Adler1, Ingela Parmrydcall_made
- external pageMulti-image colocalization and its statistical significance. Fletcher PA, Scriven DR, Schulson MN, Moore ED.call_made
2009
2007
2006
- external pageA guided tour into subcellular colocalization analysis in light microscopy S. Bolte & F. P. Cordelierescall_made
- external pageA Guide to Accurate Fluorescence Microscopy Colocalization Measurements Jonathan W. D. Comeau, Santiago Costantino, and Paul W. Wisemancall_made
- external pageColocalization Analysis Ziegler U, Aemisegger Ccall_made
2005
2004
- external pageColocalization Analysis Yields Superior Results After Image Restoration Lukas Landmann and Permsin Marbetcall_made
- external pageAutomatic and quantitative measurement of protein-protein colocalization in live cells. Costes SV, Daelemans D, Cho EH, Dobbin Z, Pavlakis G, Lockett S.call_made
Deep Learning / Artificial intelligence
2021
- external pageEvaluation and development of deep neural networks for image super-resolution in optical microscopy. Chang Qiao, Di Li, Yuting Guo, Chong Liu, Tao Jiang, Qionghai Dai, Dong Licall_made
- external pageImproving axial resolution in Structured Illumination Microscopy using deep learning. Miguel A Boland, Edward A K Cohen, Seth R Flaxman, Mark A A Neilcall_made
2020
- external pageZeroCostDL4Mic: an open platform to simplify access and use of Deep-Learning in Microscopy Lucas von Chamier, Johanna Jukkala, Christoph Spahn, Martina Lerche, Sara Hernández-Pérez, Pieta K. Mattila, Eleni Karinou, Seamus Holden, Ahmet Can Solak, Alexander Krull, Tim-Oliver Buchholz, Florian Jug, Loïc A Royer, Mike Heilemann, Romain F. Laine, Guillaume Jacquemet, and Ricardo Henriquescall_made
- external pageDeepFRET, a software for rapid and automated single-molecule FRET data classification using deep learning. Johannes Thomsen, Magnus Berg Sletfjerding, Simon Bo Jensen, Stefano Stella, Bijoya Paul, Mette Galsgaard Malle, Guillermo Montoya, Troels Christian Petersen, Nikos S Hatzakiscall_made
- Deep learning enables structured illumination microscopy with low light levels and enhanced speed. Luhong Jin, Bei Liu, Fenqiang Zhao, Stephen Hahn, Bowei Dong, Ruiyan Song, Timothy C. Elston, Yingke Xu & Klaus M. Hahn
- external pageAutomatic microscopic image analysis by moving window local Fourier Transform and Machine Learning. Jany BR, Janas A, Krok F.call_made
2019
- external pageNoise2Void - Learning Denoising from Single Noisy Images Alexander Krull, Tim-Oliver Buchholz, Florian Jugcall_made
- external pageAI-powered transmitted light microscopy for functional analysis of live cells. Kim D, Min Y, Oh JM, Cho YKcall_made
- external pageApplications, promises, and pitfalls of deep learning for fluorescence image reconstruction. Belthangady C, Royer LA.call_made
- external pageA machine learning approach for online automated optimization of super-resolution optical microscopy. Durand A, Wiesner T, Gardner MA, Robitaille LÉ, Bilodeau A, Gagné C, De Koninck P, Lavoie-Cardinal F.call_made
- external pageDeep learning enables cross-modality super-resolution in fluorescence microscopy. Wang H, Rivenson Y, Jin Y, Wei Z, Gao R, Günaydın H, Bentolila LA, Kural C, Ozcan A.call_made
2018
- external pageNoise2Noise: Learning Image Restoration without Clean Data. Jaakko Lehtinen, Jacob Munkberg, Jon Hasselgren, Samuli Laine, Tero Karras, Miika Aittala, Timo Ailacall_made
- external pageContent-aware image restoration: pushing the limits of fluorescence microscopy. Weigert M, Schmidt U, Boothe T, Müller A, Dibrov A, Jain A, Wilhelm B, Schmidt D, Broaddus C, Culley S, Rocha-Martins M, Segovia-Miranda F, Norden C, Henriques R, Zerial M, Solimena M, Rink J, Tomancak P, Royer L, Jug F, Myers EWcall_made
Special interest
2021
2020
2019
- external pageDeformed alignment of super-resolution images for semi-flexible structures. Shi X, Garcia G 3rd, Wang Y, Reiter JF, Huang B.call_made
- external pageQuantitative analysis of super-resolved structures using ASAP. Danial JSH, Garcia-Saez AJ.call_made
2018
2017
2015
2014
- external pageAdaptive fluorescence microscopy by online feedback image analysis. Tischer C, Hilsenstein V, Hanson K, Pepperkok R.call_made
- external pageDetermining absolute protein numbers by quantitative fluorescence microscopy. Verdaasdonk JS, Lawrimore J, Bloom K.call_made
2011
- external pageMicropilot: automation of fluorescence microscopy-based imaging for systems biology. Conrad C, Wünsche A, Tan TH, Bulkescher J, Sieckmann F, Verissimo F, Edelstein A, Walter T, Liebel U, Pepperkok R, Ellenberg J.call_made
- external pageTimeLapseAnalyzer: Multi-target analysis for live-cell imaging and time-lapse microscopy. Huth J, Buchholz M, Kraus JM, Mølhave K, Gradinaru C, Wichert GV, Gress TM, Neumann H, Kestler HA.call_made
- external pageSingle-virus tracking in live cells. Rust MJ, Lakadamyali M, Brandenburg B, Zhuang X.call_made
2009
- external pageAn approach for extensibly profiling the molecular states of cellular subpopulations. Loo LH, Lin HJ, Steininger RJ 3rd, Wang Y, Wu LF, Altschuler SJ.call_made
- external pageQuantifying cellular interaction dynamics in 3D fluorescence microscopy data Frederick Klauschen, Masaru Ishii, Hai Qi, Marc Bajenoff, Jackson G Egen, Ronald N Germain & Martin Meier-Schellersheimcall_made
2008
- external pageSpatial quantitative analysis of fluorescently labeled nuclear structures: Problems, methods, pitfalls O. Ronneberger, D. Baddeley, F. Scheipl, P. J. Verveer, H. Burkhardt, C. Cremer, L. Fahrmeir T, Cremer & B. Joffecall_made
- external pageAutomated classification of mitotic phenotypes of human cells using fluorescent proteins. Harder N, Eils R, Rohr K.call_made
2007