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

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]