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Table 5 A summary of software packages encountered during this literature survey

From: Survey statistics of automated segmentations applied to optical imaging of mammalian cells

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]
  1. Tool Availability options are (P)roprietary, (E)xecutable Available, (S)ource Available