Biomedical Image Informatics Lab

PI: Michael Jyh-Ying Peng (


MicroP3D software for high-content analysis of 3D mitochondrial morphology

MicroP3D 1.0a (Windows 32-bit)

MicroP3D 1.0a (Windows 64-bit)

Test data for cell segmentation: blood cell microscopic field, lymphoblast-like cell microscopic field

Test data for cell feature extraction: single blood cell images, single lymphoblast-like cell images

Cell segmentation screenshot:


Cell feature calculation screenshot:





MicroP software for high-content analysis of 2D mitochondrial morphology

MicroP 1.1.11b (Windows 32-bit)

MicroP 1.1.11b (Windows 64-bit)

Test data

Citation: Peng, J.-Y., Lin, C.-C., Chen, Y.-J., Kao, L.-S., Liu, Y.-C., Chou, C.-C., Huang, Y.-H., Chang, F.-R., Wu, Y.-C., Tsai, Y.-S. and Hsu, C.-N. (2011). Automatic Morphological Subtyping Reveals New Roles of Caspases in Mitochondrial Dynamics. PLoS Computational Biology, 7(10), e1002212-.






PombeX software for robust segmentation of Schizosaccharomyces pombe (fission yeast) cells

PombeX 1.0a (Windows 32-bit)

PombeX 1.0a (Windows 64-bit)

Test data

Citation: Peng J.-Y., Chen Y.-J., Green M.D., Sabatinos S.A., Forsburg S.L., Hsu C.-N. (2013) PombeX: Robust Cell Segmentation for Fission Yeast Transillumination Images. PLoS ONE, 8(12): e81434.




All software are developed on MATLAB R2010b, for computers without MATLAB or with an earlier version, please download and install the following MCRInstaller:

MCRInstaller (Windows 32-bit)

MCRInstaller (Windows 64-bit)


State Space Models Toolbox for MATLAB

Project page on SourceForge

Citation: Peng, J.-Y. and Aston, J. A. (2011). The State Space Models toolbox for MATLAB. Journal of Statistical Software, 41(6), 1-26.