Phase contrast microscopy (PCM) is widely used as the de facto light microscopy modality for the inspection of adherent cell cultures. PCM enables the observation of transparent cellular specimens by transforming phase shifts (induced by differences in refractive index between the sample and the surrounding medium) into changes in amplitude, which are readily detectable by the human eye or a digital camera. Automated segmentation of PCM images is made challenging by artefacts that are intrinsic to the method. The ‘shade-off effect’ results in low contrast between the interior of cellular objects and the image background, and bright halo artefacts around cellular objects commonly occur.
Enables cell lineage tracking. MicrobeTracker utilizes cell shape and timelapse information to achieve cell outlining. It can track fluorescently labeled molecules in cell lineages over several generations or in difficult-to-resolve samples, such as densely-packed or filamentous cells, from time-lapse sequences. This tool is delivered with an accessory tool, called SpotFinder, that detects small round spots, generating precise cell coordinates of fluorescently labeled foci inside cells.
Serves for effective segmentation of multidimensional datasets. MIB can recognize several number of imaging formats and offers a variety of image processing tools. It also simplifies utilization and quantification of acquired data. It permits users to segment large datasets, to realize 3D visualization, and to quantify images and models. Its parameters enable users to insert plugin s to customize the program for specific needs.
An integrated graphical user interface written in MATLAB that implements methods for automating cell segmentation/lineage reconstruction. The automated analysis iteratively combines a set of extended morphological methods for segmentation, and uses a neighborhood-based scoring method for frame-to-frame lineage linking.
An automated segmentation method that accurately separates cells when confluent and touching each other. This technique is successfully applied to phase contrast, bright field, fluorescence microscopy and binary images. The method is based on morphological watershed principles with two new features to improve accuracy and minimize over-segmentation. First, FogBank uses histogram binning to quantize pixel intensities which minimizes the image noise that causes over-segmentation. Second, FogBank uses a geodesic distance mask derived from raw images to detect the shapes of individual cells, in contrast to the more linear cell edges that other watershed-like algorithms produce.
Offers a platform for high content image analysis. CellVigene is an application made for the quantitation signal intensity and area in multiple channel or level. It includes features for automating the detection of micronuclei and nuclei, for quantifying pathologies as well as to perform mitotic spindle localization. This software can also be used for tissue microarray analysis and includes a module for 3D visualization of a composite image.
Segments nearly elliptic objects via parametric active contour. E-Snake applies an active contour (named snake) segmentation method by using exponential splines as basis functions to represent the outline of the shape. This ImageJ plugin emulates elliptical and circular shapes and can produce an approximation of any closed curve in the plane. These proprieties can be useful to delineate cross sections of cylindrical-like conduits and to outline blob-like objects.
Assists in exploration of possible watershed segmentation. Interactive-H-Watershed is a plugin for the image analysis software ImageJ. It provides an interactive way to explore local minima (maxima) on the fly. This module is based on Watershed, a common tool to segment objects in an 2D and 3D images. The method permits to gradually flood the valleys starting from their lowest point.