CellProfiler 3.0: Next-generation image processing for biology

Blastocyst-like structures generated solely from stem cells

(2018) Nicolas C. Rivron et al.   NATURE

MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy

(2017) David Svoboda et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

KNIME for reproducible cross-domain analysis of life science data

(2017) Alexander Fillbrunn et al.   JOURNAL OF BIOTECHNOLOGY

Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization

(2017) Brock Roberts et al.   MOLECULAR BIOLOGY OF THE CELL

An objective comparison of cell-tracking algorithms

(2017) Vladimír Ulman et al.   NATURE METHODS

Data-analysis strategies for image-based cell profiling

(2017) Juan C Caicedo et al.   NATURE METHODS

Systematic morphological profiling of human gene and allele function via Cell Painting

(2017) Mohammad Hossein Rohban et al.   eLife

Image-based ex-vivo drug screening for patients with aggressive haematological malignancies: interim results from a single-arm, open-label, pilot study

(2017) Berend Snijder et al.   Lancet Haematology

Automated Training of Deep Convolutional Neural Networks for Cell Segmentation

(2017) Sajith Kecheril Sadanandan et al.   Scientific Reports

Applications in image-based profiling of perturbations

(2016) Juan C Caicedo et al.   CURRENT OPINION IN BIOTECHNOLOGY

Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes

(2016) Mark-Anthony Bray et al.   Nature Protocols

'Cell painting highlights responses to drugs and toxins

(2016) E. Pennisi   SCIENCE

Deep learning

(2015) Yann LeCun et al.   NATURE

Two-pore channels control Ebola virus host cell entry and are drug targets for disease treatment

(2015) Yasuteru Sakurai et al.   SCIENCE

Review of free software tools for image analysis of fluorescence cell micrographs

(2014) V. WIESMANN et al.   JOURNAL OF MICROSCOPY

Identification of Host-Targeted Small Molecules That Restrict Intracellular Mycobacterium tuberculosis Growth

(2014) Sarah A. Stanley et al.   PLoS Pathogens

Niche-based screening identifies small-molecule inhibitors of leukemia stem cells

(2013) Kimberly A Hartwell et al.   Nature Chemical Biology

Identification of Regulators of Polyploidization Presents Therapeutic Targets for Treatment of AMKL

(2012) Qiang Wen et al.   CELL

Annotated high-throughput microscopy image sets for validation

(2012) Vebjorn Ljosa et al.   NATURE METHODS

Biological imaging software tools

(2012) Kevin W Eliceiri et al.   NATURE METHODS

Visualization and Analysis of 3D Microscopic Images

(2012) Fuhui Long et al.   PLoS Computational Biology

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software

(2011) Lee Kamentsky et al.   BIOINFORMATICS

Generation of digital phantoms of cell nuclei and simulation of image formation in 3D image cytometry

(2009) David Svoboda et al.   CYTOMETRY PART A