Computational framework for simulating fluorescence microscope images with cell populations

A Lehmussola, P Ruusuvuori… - IEEE transactions on …, 2007 - ieeexplore.ieee.org
Fluorescence microscopy combined with digital imaging constructs a basic platform for
numerous biomedical studies in the field of cellular imaging. As the studies relying on …

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

D Svoboda, M Kozubek… - … Part A: The Journal of the …, 2009 - Wiley Online Library
Image cytometry still faces the problem of the quality of cell image analysis results.
Degradations caused by cell preparation, optics, and electronics considerably affect most …

MitoGen: a framework for generating 3D synthetic time-lapse sequences of cell populations in fluorescence microscopy

D Svoboda, V Ulman - IEEE transactions on medical imaging, 2016 - ieeexplore.ieee.org
The proper analysis of biological microscopy images is an important and complex task.
Therefore, it requires verification of all steps involved in the process, including image …

BlobFinder, a tool for fluorescence microscopy image cytometry

A Allalou, C Wählby - Computer methods and programs in biomedicine, 2009 - Elsevier
Images can be acquired at high rates with modern fluorescence microscopy hardware,
giving rise to a demand for high-speed analysis of image data. Digital image cytometry, ie …

ggCyto: next generation open-source visualization software for cytometry

P Van, W Jiang, R Gottardo, G Finak - Bioinformatics, 2018 - academic.oup.com
Motivation Open source software for computational cytometry has gained in popularity over
the past few years. Efforts such as FlowCAP, the Lyoplate and Euroflow projects have …

Introduction to the quantitative analysis of two-dimensional fluorescence microscopy images for cell-based screening

V Ljosa, AE Carpenter - PLoS computational biology, 2009 - journals.plos.org
Modern automated microscopes collect digital images at an astonishing pace. Automated
image analysis can measure biological phenotypes quantitatively and reliably, and has …

An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy

F Buggenthin, C Marr, M Schwarzfischer, PS Hoppe… - BMC …, 2013 - Springer
Background In recent years, high-throughput microscopy has emerged as a powerful tool to
analyze cellular dynamics in an unprecedentedly high resolved manner. The amount of data …

An open-source solution for advanced imaging flow cytometry data analysis using machine learning

H Hennig, P Rees, T Blasi, L Kamentsky, J Hung… - Methods, 2017 - Elsevier
Imaging flow cytometry (IFC) enables the high throughput collection of morphological and
spatial information from hundreds of thousands of single cells. This high content, information …

Image segmentation and dynamic lineage analysis in single‐cell fluorescence microscopy

Q Wang, J Niemi, CM Tan, L You… - Cytometry Part A: The …, 2010 - Wiley Online Library
An increasingly common component of studies in synthetic and systems biology is analysis
of dynamics of gene expression at the single‐cell level, a context that is heavily dependent …

Analysis of live cell images: Methods, tools and opportunities

TA Nketia, H Sailem, G Rohde, R Machiraju, J Rittscher - Methods, 2017 - Elsevier
Advances in optical microscopy, biosensors and cell culturing technologies have
transformed live cell imaging. Thanks to these advances live cell imaging plays an …