Table 1.
Summary of open-source software discussed in this review
| Software Name | Primary Function | Website |
|---|---|---|
| µManager | Microscope Acquisition | http://www.micro-manager.org |
| ScanImage | Microscope Acquisition | http://www.scanimage.org |
| OMERO | Image Database | http://www.openmicroscopy.org |
| Bisque | Image Database | http://www.bioimage.ucsb.org/bisque |
| OMERO.searcher | Image Content Search | http://murphylab.web.cmu.edu/software/searcher |
| Bio-Formats | Image Format Conversion | http://www.openmicroscopy.org |
| ImageJ | Image Analysis | http://www.imagej.nih.gov |
| Fiji | Image Analysis | http://www.fiji.sc |
| BioImageXD | Image Analysis | http://www.bioimagexd.net |
| Icy | Image Analysis | http://icy.bioimageanalysis.org |
| CellProfiler | Image Analysis | http://www.cellprofiler.org |
| Vaa3D | Visualization and Image Analysis | http://www.vaa3d.org |
| FarSight | Visualization | http://www.farsight-toolkit.org/ |
| Visualization Tool Kit (VTK) | Bioimaging library | http://www.vtk.org |
| Insight Tool Kit (ITK) | Bioimaging library | http://www.itk.org |
| OpenCV | Bioimaging library | http://opencv.willowgarage.com/wiki/ |
| WND-CHARM | Machine learning | http://code.google.com/p/wnd-charm/ |
| PSLID | Machine learning | http://pslid.org |
| Ilastik | Machine learning | http://www.ilastik.org/ |
| CellProfiler Analyst | Machine learning and data analysis | http://www.cellprofiler.org |
| PatternUnmixer | Machine learning | http://murphylab.web.cmu.edu/software |
| CellOrganizer | Machine learning, modeling, visualization | http://CellOrganizer.org |
| KNIME | Workflow system | http://www.knime.org/ |