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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 [137139] 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/