Image Processing, Quantitative Microscopy, Colocalisation

General

2024

• external page A guide to single-particle tracking François Simon, Lucien E. Weiss & Sven van Teeffelen

2017

• external page Analysis of live cell images: Methods, tools and opportunities. Nketia TA, Sailem H, Rohde G, Machiraju R, Rittscher J

• external page Single Particle Tracking: From Theory to Biophysical Applications Shen H, Tauzin LJ, Baiyasi R, Wang W, Moringo N, Shuang B, Landes CF

• external page A BaSiC tool for background and shading correction of optical microscopy images Peng T, Thorn K, Schroeder T, Wang L, Theis FJ, Marr C, Navab N

2016

• external page Image Quality Ranking Method for Microscopy. Sami Koho, Elnaz Fazeli, John E. Eriksson, & Pekka E. Hänninen

2013

• external page Post-processing for statistical image analysis in light microscopy. Cardullo RA, Hinchcliffe EH.

• external page Quantitative analysis of digital microscope images. Wolf DE, Samarasekera C, Swedlow JR.

• external page 65,000 shades of grey: use of digital image files in light microscopy. Shaw SL, Hinchcliffe EH.

2012

• external page Biological 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.

• external page Open source tools for fluorescent imaging. Hamilton NA.

• external page Software tools, data structures, and interfaces for microscope imaging. Stuurman N, Swedlow JR.

2009

• external page Accuracy and precision in quantitative fluorescence microscopy. Waters JC.

• external page Quantification and its applications in fluorescent microscopy imaging. Hamilton N.
  

2007

• external page ImageJ for microscopy. Collins TJ.

2006

• external page Seeing is believing? A beginners’ guide to practical pitfalls in image acquisition North, A

• external page CellProfiler: 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 DM

2000

• external page The 39 steps: a cautionary tale of quantitative 3-D fluorescence microscopy Pawley J.
  

1995

• external page A pixel is not a little suare Smith, AR

Colocalization

2019

• external page ColocalizR: An open-source application for cell-based high-throughput colocalization analysis. Sauvat A, Leduc M, Müller K, Kepp O, Kroemer G.

2015

• external page Quantifying molecular colocalization in live cell fluorescence microscopy. Fabian Humpert, Idir Yahiatene, Martina Lummer, Markus Sauer, and Thomas Huser

2014

• external page Experimenters' guide to colocalization studies: Finding a way through indicators and quantifiers, in practice. Cordelières FP, Bolte S.

2013

• external page A novel method for quantified, superresolved, three-dimensional colocalisation of isotropic, fluorescent particles. Obara B1, Jabeen A, Fernandez N, Laissue PP.

• external page Colocalization Analysis in Fluorescence Microscopy. Jeremy Adler and Ingela Parmryd

• external page Colocalisation Workshop Imaging Core Facility Biozentrum Basel. Ferrand A.

• external page A novel method for quantified, superresolved, three-dimensional colocalisation of isotropic, fluorescent particles. Obara B, Jabeen A, Fernandez N, Laissue PP.

• external page Colocalization analysis in fluorescence microscopy. Adler J, Parmryd I.

• external page New image colocalization coefficient for fluorescence microscopy to quantify (bio-)molecular interactions. Herce HD, Casas-Delucchi CS, Cardoso MC.
  

2012

• external page Coordinate-based colocalization analysis of single-molecule localization microscopy data. Malkusch S, Endesfelder U, Mondry J, Gelléri M, Verveer PJ, Heilemann M.

2011

• external page A practical guide to evaluating colocalization in biological microscopy. Dunn KW, Kamocka MM, McDonald JH.
  

2010

• external page Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. Jo A Helmuth, Grégory Paul, and Ivo F Sbalzarini

• external page Quantifying Colocalization by Correlation: The Pearson Correlation Coefficient is Superior to the Mander’s Overlap Coefficient Jeremy Adler, Ingela Parmryd

• external page Quantifying Colocalization: Thresholding, Void Voxels and the Hcoef Jeremy Adler1, Ingela Parmryd

• external page Multi-image colocalization and its statistical significance. Fletcher PA, Scriven DR, Schulson MN, Moore ED.

2009

• external page Automated organelle-based colocalization in whole-cell imaging. Woodcroft BJ, Hammond L, Stow JL, Hamilton NA.

2007

• external page Quantitative colocalization analysis of multicolor confocal immunofluorescence microscopy images: pushing pixels to explore biological phenomena. Zinchuk V, Zinchuk O, Okada T.

2006

• external page A guided tour into subcellular colocalization analysis in light microscopy S. Bolte & F. P. Cordelieres

• external page A Guide to Accurate Fluorescence Microscopy Colocalization Measurements Jonathan W. D. Comeau, Santiago Costantino, and Paul W. Wiseman

• external page Colocalization Analysis Ziegler U, Aemisegger C
  

2005

• external page An automated method to quantify and visualize colocalized fluorescent signals. Jaskolski F, Mulle C, Manzoni OJ
  

2004

• external page Colocalization Analysis Yields Superior Results After Image Restoration Lukas Landmann and Permsin Marbet

• external page Automatic and quantitative measurement of protein-protein colocalization in live cells. Costes SV, Daelemans D, Cho EH, Dobbin Z, Pavlakis G, Lockett S.

Deep Learning / Artificial intelligence

2025

• external page Deep Learning-Based Image Restoration and Super-Resolution for Fluorescence Microscopy: Overview and Resources David Lohr, Lina Meyer, Lena-Marie Woelk, Dejan Kovacevic, Bjorn-Philipp Diercks, and Rene Werner

2023

• external page Live-cell imaging in the deep learning era Joanna W Pylvänäinen, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Guillaume Jacquemet

• external page Deep learning enables fast, gentle STEDmicroscopy Vahid Ebrahimi, Kyu Young, Han,Till StephanJiah Kim4, Pablo Carravilla, Christian Eggeling, Stefan Jakobs, Kyu Young Han  

• external page Single-frame deep-learning super-resolution microscopy for intracellular dynamics imaging Rong Chen, Xiao Tang, Yuxuan Zhao, Zeyu Shen, Meng Zhang, Yusheng Shen, Casper Ho Yin Chung, Lijuan Zhang, Ji Wang, Binbin Cui, Peng Fei, Yusong Guo, Shengwang Du, Shuhuai Yao

2021

• external page Evaluation 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 Li

• external page Improving axial resolution in Structured Illumination Microscopy using deep learning. Miguel A Boland, Edward A K Cohen, Seth R Flaxman, Mark A A Neil

2020

• external page ZeroCostDL4Mic: 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 Henriques

• external page DeepFRET, 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 Hatzakis

• 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 page Automatic microscopic image analysis by moving window local Fourier Transform and Machine Learning. Jany BR, Janas A, Krok F.
  

2019

• external page Noise2Void - Learning Denoising from Single Noisy Images Alexander Krull, Tim-Oliver Buchholz, Florian Jug

• external page AI-powered transmitted light microscopy for functional analysis of live cells. Kim D, Min Y, Oh JM, Cho YK

• external page Applications, promises, and pitfalls of deep learning for fluorescence image reconstruction. Belthangady C, Royer LA.

• external page A 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.

• external page Deep 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.
  

2018

• external page Noise2Noise: Learning Image Restoration without Clean Data. Jaakko Lehtinen, Jacob Munkberg, Jon Hasselgren, Samuli Laine, Tero Karras, Miika Aittala, Timo Aila

• external page Content-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 EW
  

Special interest

2021

• external page CellProfiler 4: improvements in speed, utility and usability. David R Stirling, Madison J Swain-Bowden, Alice M Lucas, Anne E Carpenter, Beth A Cimini, Allen Goodman

2020

• external page CytoSeg 2.0: automated extraction of actin filaments. Nowak J, Gennermann K, Persson S, Nikoloski Z.

2019

• external page Deformed alignment of super-resolution images for semi-flexible structures. Shi X, Garcia G 3rd, Wang Y, Reiter JF, Huang B.

• external page Quantitative analysis of super-resolved structures using ASAP. Danial JSH, Garcia-Saez AJ.

2018

• external page VirusMapper: open-source nanoscale mapping of viral architecture through super-resolution microscopy. Gray RD, Beerli C, Pereira PM, Scherer KM, Samolej J, Bleck CK, Mercer J, Henriques R.
  

2017

• external page Single Particle Tracking: From Theory to Biophysical Applications Shen H, Tauzin LJ, Baiyasi R, Wang W, Moringo N, Shuang B, Landes CF

2015

• external page CellProfiler: Novel Automated Image Segmentation Procedure for Super-Resolution Microscopy. Soliman K.

2014

• external page Adaptive fluorescence microscopy by online feedback image analysis. Tischer C, Hilsenstein V, Hanson K, Pepperkok R.

• external page Determining absolute protein numbers by quantitative fluorescence microscopy. Verdaasdonk JS, Lawrimore J, Bloom K.

2011

• external page Micropilot: 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.

• external page TimeLapseAnalyzer: 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.

• external page Single-virus tracking in live cells. Rust MJ, Lakadamyali M, Brandenburg B, Zhuang X.
  

2009

• external page An approach for extensibly profiling the molecular states of cellular subpopulations. Loo LH, Lin HJ, Steininger RJ 3rd, Wang Y, Wu LF, Altschuler SJ.

• external page Quantifying cellular interaction dynamics in 3D fluorescence microscopy data Frederick Klauschen, Masaru Ishii, Hai Qi, Marc Bajenoff, Jackson G Egen, Ronald N Germain & Martin Meier-Schellersheim

2008

• external page Spatial 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. Joffe

• external page Automated classification of mitotic phenotypes of human cells using fluorescent proteins. Harder N, Eils R, Rohr K.
  

2007

• external page Linear fluorescence unmixing in cell biological research Birgit Kraus , Manja Ziegler and Horst Wolff