Bioimage Analyst

This plugin tags all pixel/voxels in a skeleton image and then counts all its junctions, triple and quadruple points and branches, and measures their average and maximum length.


he tags are shown in a new window displaying every tag in a different color. You can find it under [Plugins>Skeleton>Analyze Skeleton (2D/3D)]. See Skeletonize3D for an example of how to produce skeleton images.

Clustered cell nuclei

One of the principal challenges in counting or segmenting cells or cell nuclei is dealing with clustered objects. To help assess algorithms' performance in this regard, synthetic 3D image sets of HL60 cell line are provided consisting of four subsets with increasing degree of clustering. Each subset is also provided in two diferent levels of quality: high SNR and low SNR.Ground truth is available as well.

spot detection and codistribution analysis

WASH, Exo84, and cortactin spot detection and codistribution analysis To detect endosomes, an automatic Otsu threshold is applied to the Gaussian-filtered MT1-MMP–positive endosome image (= 1.5 pixels for the sample image). Statistics about each endosome are then saved, for example random positioning of spots can be compared to actual positioning. For each endosome, WASH and Exo84 (or WASH and cortactin) spots are searched for in a neighboring of x pixels in their respective channel.