MicroSCoBioJ is a collection of three plugins to create and visualize 3D fluorescence volume rendering
Fabio Frosi (frogsi (at) libero.it)
Giuseppe Vicidomini (gvicid (at) gwdg.de)
Requires: ImageJ + Java 3D ( http://java3d.j3d.org/download.html )
Limitations: Only works with 8-bit images stack
MicroSCoBioJ contains three plugins:
The algorithm used in the previous step, identifies a global threshold for all pixels of an image, using statistical properties of the image histogram. Unfortunately this algorithm is not able to accommodate changes in the distribution of different fluorescence concentration in a structure. Chow and Kaneko (ref. 1) solved this problem dynamically changing the threshold over the image: each local pixel threshold is obtained by statistical investigation of the intensity values of the local neighbourhoods of such pixel. We combined the IsoData threshold (Th_IsoD) (ref. 2), with the dynamic threshold (Thd), to find a weight adaptive threshold (Thwa): Thwa(x,y) = wIsoD* ThIsoD + wd *Thd(x,y) + wbase*Thbase+background with wIsoD + wd + wbase= 1 Thbase can be used to increase or decrease the final threshold on the base of prior information; moreover, further information, e.g. background, can be directly added to the algorithm.
Using WAT MicroScoBioJ menu one can choose the following parameters: the window size, Thbase , three weights and the background value.
Download MicroSCoBiOJ.zip and unzip it into the plugins folder and restart ImageJ.