GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images

Table 1 Comparison between softwares available for cell segmentation

Property	GoIFISH	Columbus	CellProfiler	ImageJ	ImageM	CellTracker
Cost	Open-Source	Proprietary	Open-Source	Open-Source	Open-Source on request	Open-Source
Real-Time Update	Yes	Yes	No	No	No	Yes
Background Intensity Subtraction	Yes	Tuning but no subtraction	Correct Illumination Calculate	Flatten Illumination	No	No
A-Priori knowledge required (eg. cell size or segmentation methods)	No	No	Yes	No	No	No
Nuclear Segmentation	Yes	Yes	Yes	Yes	Manual	Yes
Membrane Segmentation	Yes	Yes	Yes	Yes	Manual	Yes
Spot Detection	Yes	Yes	Yes	Yes	Yes	No
Batch Processing	CmdLine Only	Yes	Yes	BatchCommand Plugin	No	No
Visualise Batch Segmentation Results	Yes	No	Yes	No	No	No
Manual Editing	Yes	No	No	No	Yes	Yes
Cell Specific Information	Yes	Yes	Yes	Yes	Yes	Yes
Summary Report	Yes	Yes	Yes	Yes	Yes	Yes
Topology or summary Maps	Yes	No	Yes	Topit Plugin	No	No

ISSN: 1474-760X