Survey Statistics of Automated Segmentations Applied to Optical Imaging of Mammalian Cells

Classification of 72 publications according to the classification criteria described below. The image segmentation-related publications are at the intersection of optical microscopy-based cellular measurements and automated segmentation.

The first order (frequency of occurrence) and second order (co-occurrence) statistics derived from classifications of the surveyed literature consist of three layers of information:

(1) a list of classification categories and their occurrences,

(2) a table of co-occurring categories and their co-occurrences, and

(3) the list of papers that are contributing to each occurrence or co-occurrence number. These three layers of information would not fit into this manuscript and are easier to browse as a set of web hyperlinked web pages.

Access to 1st Order (Histogram) and 2nd Order (Co-Occurrence) Statistics of Classification Categories Applied to the Surveyed Publications

Access to 1st and 2nd Order Stats Object of Interest Imaging Modality Data Axes Segmentation Segmentation Evaluation Segmentation Acceleration Platform Object Measurement

Object of Interest Click Click Click Click Click Click

Imaging Modality Click Click Click Click Click

Data Axes Click Click Click Click

Segmentation Click Click Click

Segmentation Evaluation Click Click

Segmentation Acceleration Platform Click

Object Measurement

Classification Categories and Their Sub-categories Applied to the Surveyed Publications

Object of Interest	Imaging Modality	Data Axes	Segmentation	Segmentation Evaluation	Segmentation Acceleration Platform	Object Measurement
Cell	Phase Contrast	X-Y-T	Thresholding	Visual inspection	Unknown	Motility
Nucleus	Differential Interference Contrast	X-Y-Z	Region Growing	Unknown	Single-core Central Processing Unit (CPU)	Counting
Synthetic (digital model)	Bright-field	X-Y-Z-T	Morphological	Technique is not specified	Multi-core CPU	Geometry
Synthetic (reference material)	Dark-field		Watershed	Object-level evaluation	Graphics Processing Unit (GPU)	Location
Other (proteins, fibers, extracellular space, etc.)	Confocal fluorescence		Graph-based	Pixel-level evaluation	Cluster	Intensity
	Wide-field fluorescence		Active contours & Level Set
	Two-photon fluorescence		Partial Derivative Equations (PDE)
	Light sheet		Other

Survey publication disclaimer:

The National Institute of Standards and Technology (NIST) uses substantial efforts to select publications that meet the publication survey criteria. However, NIST makes no warranties that the survey is exhaustive. The survey and its contents are provided by NIST as a public service and are strictly provided "AS IS" with no warranties of any type. Furthermore, NIST does not make any statements about quality of publications by including them in the survey classification and does not imply any recommendation or endorsement.

Contributors:

ITL-Software and Systems Division

Information Systems Group

MML-Biosystems and Biomaterials Division

Cell Systems Science Group

Lodz University of Technology, Poland

Marcin Kociolek

Publications:

Authors, "Survey Statistics of Automated Segmentations Applied to Optical Imaging of Mammalian Cells", BMC Bioinformatics, 2015, 16:330. doi: 10.1186/s12859-015-0762-2 (pdf)

Data Download:

(download Tab delimited txt file)

Contact:

Peter Bajcsy
peter.bajcsy@nist.gov
Phone: 301.975.2958

Access to 1st and 2nd Order Stats	Object of Interest	Imaging Modality	Data Axes	Segmentation	Segmentation Evaluation	Segmentation Acceleration Platform	Object Measurement
Object of Interest		Click	Click	Click	Click	Click	Click
Imaging Modality			Click	Click	Click	Click	Click
Data Axes				Click	Click	Click	Click
Segmentation					Click	Click	Click
Segmentation Evaluation						Click	Click
Segmentation Acceleration Platform							Click
Object Measurement