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