Image segmentation

WIS-PhagoTracker is a software application for quantitative analysis of high throughput cell migration assay. The cell migration assay is based on a modified Phagokinetic tracks procedure, in which motile cells "leave their tracks" on a specialized surface. These tracks are visualized using a screening microscope.

WIS-PhagoTracker enables morphometric analysis of such tracks. It uses multiscale segmentation algorithm for fine detection of tracks and cells boundaries.

Following the segmentation step, it quantifies various morphometric parameters for each track, such as track area, perimeter, major and minor axis and solidity. All these measures are calculated for each track in each well of a well plate and saved for further statistical analysis WIS-PhagoTracker supports all the analysis phases starting from preprocessing, finding tracks of selected wells or a whole plate, through viewing the results and manually rejecting tracks to statistical analysis of the results. It also supports batch processing of several plates, and analysis of single image files. A user interface enables the user to modify the relevant parameters of the process, according to specific image's requirements.

Results are exported into Excel readable files.

WIS-NeuroMath - is a software tool for automated analysis and quantification of fluorescent microscopy images of Nerve cells, in both in vivo and in vitro preparations. It allows for accurate detection of neurites in challenging images. Following neurite detection, different types of processing can be carried: Cell Morphology of cultured neurons, Neurite Length Analysis and Ganglion Explant Analysis. Usefull also for angiogenesis analysis.

This plugin threshold an image using the Maximum Entropy algorithm, which aims at maximizing the inter-class entropy. Entropy is defined as -sum(p.*log2(p)), where p contains the histogram bin counts. This thresholding is very useful to segment images with few bright objects on large dark background. In ImageJ/FIJI you can acces this tool in Image->Adjust->Threshold and choose in the list In Aphelion, you can access this tool in Seglmentation->Threshold-> AphImgEntropyThreshold

Drop Shape Analysis is a collection of two methods (DropSnake and LBADSA) for high-accuracy measure of contact angles for drop measurement.

Image segmentation by representative colors selection. Two versions are available :

• thresholding
• positive and negative colors selection and SVM learning