Cytokit: a single-cell analysis toolkit for high dimensional fluorescent microscopy imaging

Assessing microscope image focus quality with deep learning

(2018) Samuel J. Yang et al.   BMC BIOINFORMATICS

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes

(2018) Jia-Ren Lin et al.   eLife

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging

(2018) Yury Goltsev et al.   CELL

Fast and accurate three-dimensional point spread function computation for fluorescence microscopy

(2017) Jizhou Li et al.   JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION

DeconvolutionLab2: An open-source software for deconvolution microscopy

(2017) Daniel Sage et al.   METHODS

Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues

(2017) Yu Wang et al.   NANO LETTERS

histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data

(2017) Denis Schapiro et al.   NATURE METHODS

Systems pathology by multiplexed immunohistochemistry and whole-slide digital image analysis

(2017) Sami Blom et al.   Scientific Reports

Mass Cytometry: Single Cells, Many Features

(2016) Matthew H. Spitzer et al.   CELL

Multispectral flow cytometry: The consequences of increased light collection

(2016) Kristen Feher et al.   CYTOMETRY PART A

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis

(2014) Greg Finak et al.   PLoS Computational Biology

scikit-image: image processing in Python

(2014) Stéfan van der Walt et al.   PeerJ

Technical issues: flow cytometry and rare event analysis

(2013) B. D. Hedley et al.   International Journal of Laboratory Hematology

flowClust: a Bioconductor package for automated gating of flow cytometry data

(2009) Kenneth Lo et al.   BMC BIOINFORMATICS

CellProfiler Analyst: data exploration and analysis software for complex image-based screens

(2008) Thouis R Jones et al.   BMC BIOINFORMATICS

Efficient subpixel image registration algorithms

(2008) Manuel Guizar-Sicairos et al.   OPTICS LETTERS