Table 5.
A summary of software packages encountered during this literature survey
| Software name | Description | Tool availability | Reference |
|---|---|---|---|
| Ilastik | A tool for interactive image classification, segmentation, and analysis | S | [135] |
| FARSIGHT | Toolkit of image analysis modules with standardized interfaces | S | [136] |
| ITK | Suite of image analysis tools | S | [137] |
| VTK | Suite of image processing and visualization tools | S | [138] |
| CellSegmentation3D | Command line segmentation tool | E | [139] |
| ImageJ/Fiji | Image processing software package consisting of a distribution of ImageJ with a number of useful plugins | E + S | [78] |
| Vaa3D | Cell visualization and analysis software package | E + S | [140] |
| CellSegM | Cell segmentation tool written in MATLAB | S | [141] |
| Free-D | Software package for the reconstruction of 3D models from stacks of images | E | [142] |
| CellExplorer | Software package to process and analyze 3D confocal image stacks of C. elegans | S | [143] |
| CellProfiler | Software package for quantitative segmentation and analysis of cells | E + S | [144] |
| Kaynig’s tool | Fully automatic stitching and distortion correction of transmission electron microscope images | E + S | [145] |
| KNIME | Integrating image processing and advanced analytics | E + S | [146] |
| LEVER | Open-source tool for segmentation and tracking of cells in 2D and 3D | S | [31, 147] |
| OMERO | Client–server software for visualization, management and analysis of biological microscope images. | E + S | [148] |
| Micro-Manager | Open-source microscope control software | E + S | [149] |
| MetaMorph | Microscopy automation and image analysis software | PE | [124] |
| Imaris | Software for data visualization, analysis, segmentation, and interpretation of 3D and 4D microscopy datasets. | PE | [150] |
| Amira | Software for 3D and 4D data processing, analysis, and visualization | PE | [151] |
| Acapella | High content imaging and analysis software | PE | [85] |
| CellTracer | Cell segmentation tool written in MATLAB | E + S | [124] |
| FogBank | Single cell segmentation tool written in MATLAB | E + S | [122] |
| ICY | Open community platform for bioimage informatics. | E + S | [65] |
| CellCognition | Computational framework dedicated to the automatic analysis of live cell imaging data in the context of High-Content Screening (HCS) | E + S | [152] |
Tool Availability options are (P)roprietary, (E)xecutable Available, (S)ource Available