Light microscopy applications in systems biology: opportunities and challenges

Antony, Paul Paul Michel Aloyse; Trefois, Christophe; Stojanovic, Aleksandar; Baumuratov, Aidos Sagatovich; Kozak, Karol

doi:10.1186/1478-811X-11-24

Cell Communication and Signaling

Table 2 Open-source software tools for image processing and analysis

From: Light microscopy applications in systems biology: opportunities and challenges

Software	Class	Extendibility & Dimensionality									Description	References	Link
		Java	Matlab	C++	Perl	Python	R	2D	3D	nD
1C1V-Nauru	Analysis	Yes	No	No	Yes	Yes	Yes	Yes	Yes	Yes	Two-dimensional visualization of image-based screening data sets from high content screening	[115]	http://knime.org/
4D Viewer	Analysis	Yes	No	No	No	No	No	No	Yes	No	Plugin for ImageJ to visualize three-dimensional image stacks	[116]	http://3dviewer.neurofly.de/
ACME	Analysis	No	No	Yes	No	No	No	No	Yes	No	Membrane-based cell segmentation and morphology analysis that has been used for embryogenesis time-lapse datasets	[117]	https://github.com/krm15/ACME
Advanced Cell Classifier	Analysis	No	Yes	No	No	No	No	Yes	No	No	Data analyzer program using machine learning methods to evaluate cell-based high-content screens	[118]	http://acc.ethz.ch/
Bisque	Processing	No	No	No	No	Yes	No	Yes	Yes	Yes	Bisque (Bio-Image Semantic Query User Environment) was developed for the exchange and exploration of biological images and is widely used in plant biology	[119, 120]	http://www.image.ucsb.edu/bisque
Bio-Formats	Processing	Yes	Yes	Yes	No	Yes	No	Yes	Yes	Yes	Standalone Java library for reading and writing life sciences image file formats	[121]	http://www.openmicroscopy.org/
BioImageXD	Analysis	No	No	Yes	No	Yes	No	Yes	Yes	No	Software for analyzing image-based high-throughput screening data	[122]	http://www.imagexd.net/
CellClassifier	Analysis	No	Yes	No	No	No	No	Yes	No	No	Matlab package of machine learning tools for the classification of cells or other biological objects	[123]	http://www.cellclassifier.ethz.ch
CellCognition	Analysis	No	No	Yes	No	Yes	No	Yes	No	No	Machine learning tool for time-resolved phenotype annotation that uses automatically extracted class transition probabilities to correct classification errors without user supervision	[33]	http://www.cellcognition.org/
CellExplorer	Analysis	No	Yes	No	No	No	No	No	Yes	No	Matlab code for a 3D digital atlas	[35]	http://penglab.janelia.org/proj/cellexplorer/
CellHTS Bioconductor	Analysis	No	No	No	No	No	Yes	Yes	Yes	Yes	Library for R-based analysis of cell based screens, visualization of screening data, statistical analysis, and connecting to other bioinformatics resources	[124]	http://www.bioconductor.org/
CellProfiler	Analysis	No	Yes	No	No	Yes	No	Yes	No	No	Image analysis platform designed for biologists without training in computer vision or programming for automated quantitative measurement of phenotypes from thousands of images	[125, 126]	http://www.cellprofiler.org/
CellProfiler Analyst	Analysis	No	No	No	No	Yes	No	Yes	Yes	No	High-level data analysis platform that supports the CellProfiler framework. CellProfiler Analyst includes tools for classification, interactive data browsing, data mining, and visualization	[127, 128]	http://www.cellprofiler.org/
EBImage	Analysis	No	No	No	No	No	Yes	Yes	Yes	No	Library of image analysis tools for the statistical programming environment R	[129]	http://www.bioconductor.org/packages/release/bioc/html/EBImage.html
FarSight	Analysis	No	No	No	No	Yes	No	Yes	Yes	Yes	Toolkit for Python-based multidimensional image analysis	[130]	http://farsight-toolkit.org
Fiji	Analysis	Yes	No	No	No	No	No	Yes	Yes	Yes	Software-engineering friendly ImageJ distribution with automated plugin management and the library ImgLib for type-, dimension-, and storage-independent representation of image data	[131]	http://fiji.sc/
iCluster	Analysis	No	No	No	No	No	No	Yes	Yes	No	Statistical tool that represents screening images in a spatial similarity layout	[132, 133]	http://icluster.imb.uq.edu.au/
Icy	Analysis	Yes	No	No	No	No	No	Yes	Yes	No	Modern user and developer friendly open image informatics platform aiming to support extended reproducible research	[134, 135]	http://icy.imageanalysis.org
Ilastik	Analysis	No	No	No	No	Yes	No	Yes	Yes	No	Pattern recognition-based image segmentation	[93, 136]	http://www.ilastik.org/
ImageJ	Analysis	Yes	No	No	No	No	No	Yes	Yes	No	Java-based extendable package of microscope image analysis tools	[137–139]	http://rsbweb.nih.gov/ij/
ImageJ2	Analysis	Yes	No	No	No	No	No	Yes	Yes	Yes	Next generation of ImageJ	[112]	http://developer.imagej.net/
ImgLib2	Analysis	Yes	No	No	No	No	No	Yes	Yes	Yes	Java library for n-dimensional data representation and manipulation with a focus on image processing	[140]	http://imglib2.net
ITK	Analysis	No	No	Yes	No	No	No	Yes	Yes	Yes	The insight segmentation and registration toolkit (ITK) is a library, initially based on C++, that performs registration and segmentation	[141]	http://www.itk.org/
KNIME	Analysis	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	The Konstanz Information Miner (KNIME) is a workflow tool for the visual assembly and interactive execution of a data pipeline	[142]	http://www.knime.org/
mRMR	Analysis	No	Yes	Yes	No	No	No	Yes	Yes	Yes	Feature classifier for minimum redundancy maximum relevance feature selection	[143]	http://penglab.janelia.org/proj/mRMR/
OME	Processing	Yes	Yes	Yes	No	Yes	No	Yes	Yes	Yes	The Open Microscopy Environment (OME) provides file formats and metadata standards for microscope images	[144, 145]	http://www.openmicroscopy.org/
OMERO	Processing	Yes	Yes	Yes	No	Yes	No	Yes	Yes	Yes	Visualization, multi user management, and analysis of biological microscopy images	[146, 147]	http://www.openmicroscopy.org/
OMERO.searcher	Processing	No	No	No	No	No	No	Yes	No	No	Tool for content-based image retrieval	[148]	http://murphylab.web.cmu.edu/software/searcher/
OpenBis	Processing	Yes	No	No	No	No	No	Yes	Yes	Yes	Management system for biological information. The main goal is to support biological research data workflows from the source (i.e., the measurement of instruments and facilitating the process of answering biological questions using cross-domain queries against raw data, processed data, knowledge resources, and metadata)	[149]	http://www.cisd.ethz.ch/software/openBIS
OpenCV	Analysis	Yes	No	Yes	No	Yes	No	Yes	No	No	Library for feature extraction, tracking, and visualization in 2D plus time	[150]	http://opencv.org/
PatternUnmixer	Analysis	No	Yes	No	No	No	No	Yes	No	No	Machine learning tool used to determine the distribution of probes between different subcellular compartments	[151, 152]	http://murphylab.web.cmu.edu/software/PatternUnmixer2.0/
PhenoRipper	Analysis	No	Yes	No	No	No	No	Yes	No	No	Image block-based tool for the rapid exploration of high content microscopy images	[153]	http://www.phenoripper.org/
Vaa3D	Analysis	No	No	Yes	No	No	No	Yes	Yes	Yes	Extendible platform for 3D visualization-assisted image analysis	[154]	http://www.vaa3d.org/
VANO	Analysis	No	No	Yes	No	No	No	Yes	Yes	No	Object annotation system for 3D multicolor image stacks	[155]	http://vano.cellexplorer.org/
VisBio	Analysis	Yes	No	No	No	No	No	Yes	Yes	Yes	Visualization and analysis of multidimensional image data	[156]	http://loci.wisc.edu/software/visbio
VTK	Analysis	No	No	Yes	No	No	No	Yes	Yes	No	The visualization toolkit (VTK) is a library of C++ code for 3D computer graphics, image processing, and visualization	[157]	http://www.vtk.org/
Voxx	Analysis	No	No	Yes	No	No	No	Yes	Yes	No	Tool for fast, GPU-based 3D rendering	[158]	http://www.indiana.edu/~voxx/index.html
WND-CHARM	Analysis	No	No	Yes	No	Yes	No	Yes	Yes	Yes	Command line program for image-based feature extraction	[159]	http://code.google.com/p/wnd-charm/

Back to article page

ISSN: 1478-811X

Contact us

General enquiries: journalsubmissions@springernature.com