Combining intensity, edge, and shape information for 2D and 3D segmentation of cell nuclei in tissue sections

Wählby, CarolinaUppsala universitet,Centrum för bildanalys,Datoriserad bildanalys (author)

We present a region-based segmentation method in which seeds representing both object and background pixels are created by combining morphological filtering of both the original image and the gradient magnitude of the image. The seeds are then used as starting points for watershed segmentation of the gradient magnitude image. The fully automatic seeding is done in a generous fashion, so that at least one seed will be set in each foreground object. If more than one seed is placed in a single object, the watershed segmentation will lead to an initial over-segmentation, i.e. a boundary is created where there is no strong edge. Thus, the result of the initial segmentation is further refined by merging based on the gradient magnitude along the boundary separating neighbouring objects. This step also makes it easy to remove objects with poor contrast. As a final step, clusters of nuclei are separated, based on the shape of the cluster. The number of input parameters to the full segmentation procedure is only five. These parameters can be set manually using a test image and thereafter be used on a large number of images created under similar imaging conditions. This automated system was verified by comparison with manual counts from the same image fields. About 90% correct segmentation was achieved for two- as well as three-dimensional images.

NATURVETENSKAP Data- och informationsvetenskap Datorseende och robotik hsv//swe
NATURAL SCIENCES Computer and Information Sciences Computer Vision and Robotics hsv//eng
Automation/methods
Cell Nucleus/*ultrastructure
Cervix Neoplasms/*pathology/ultrastructure
Female
Humans
Image Processing; Computer-Assisted/*methods
Microscopy; Fluorescence/methods
Sensitivity and Specificity
Image analysis
Bildanalys

Sintorn, Ida-MariaUppsala universitet,Centrum för bildanalys,Datoriserad bildanalys(Swepub:uu)idsin102 (author)
Erlandsson, Fredrik (author)
Borgefors, GunillaUppsala universitet,Centrum för bildanalys,Datoriserad bildanalys(Swepub:uu)gbo21123 (author)
Bengtsson, EwertUppsala universitet,Centrum för bildanalys,Datoriserad bildanalys(Swepub:uu)ewertbs (author)
Uppsala universitetCentrum för bildanalys (creator_code:org_t)

By the author/editor: Wählby, Carolina; Sintorn, Ida-Mar ...; Erlandsson, Fred ...; Borgefors, Gunil ...; Bengtsson, Ewert

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Computer and Inf ...; and Computer Vision ...

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