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Center for Biomedical Informatics, TMHRI-Weill Cornell
The ZFIQ (Zebrafish Image Quantitator) software toolkit is developed by the Medical Image Computing Group of the Center for Biomedical Informatics (CBI, Director: Dr. Stephen Wong), Methodist Hospital Research Institute with a large part of the development effort was done while Stephen’s group was part of the Harvard Center for Neurodegeneration and Repair, Harvard Medical School. The software aims to provide a set of practical and effective image analysis tools for quantitative, reproducible and accurate interpretation of zebrafish imaging data, in particular, for streamlined processing and analysis of bioimaging data. The design of ZFIQ is modular such that new applications and modules can be added into the toolkit. ZFIQ is a subset of CBI platform. CBI platform is a generic image computing software platform that could be used for processing of biological imaging data and medical imaging data, as well as other general images. ZFIQ is a collection of specific filters and pipelines developed for zebrafish image processing and analysis. ZFIQ shares the same low level image processing and analysis routines, interfaces, I/Os, and etc. of the CBI platform.
NIfTI-1 support
Future version will support NIfTI-1
Medical Image Computing Lab (Director, Tianming Liu), Center for Biomedical Informatics (Director, Stephen Wong), TMHRI-Weill Cornell
Stephen Wong:; Tianming Liu:
How to get
Download at:
Current version
Version 1.0
Current version release date
Aug.23, 2007
Open source
Available free of charge
Windows 2000, Windows XP and Windows Vista
Technical publications
1. Tianming Liu. A quantitative zebrafish phenotyping tool for developmental biology and disease modeling. IEEE Signal and Processing Magazine. 24(1):126-129. 2007
Applications publications
1. Gang Li, Tianming Liu, Ashley Tarokh, Jingxin Nie, Lei Guo, Andrew Mara, Scott Holley, Stephen TC Wong. 3D Cell Segmentation Based on Gradient Flow Tracking, accepted with revision, in press, BMC Cell Biology, 2007. 2. Gang Li, Tianming Liu, Jingxin Nie, Lei Guo, Jarema Malicki, Andrew Mara, Scott Holley, Weiming Xia, Stephen Wong. Detection of Blob Objects in Microscopic Zebrafish Images Based on Gradient Vector Diffusion, in press, Cytometry A, 2007. 3. Gang Li, Tianming Liu, Jingxin N, Guo L, Andrew M, Holley S, Zhu J, Chen J, Wong STC. Segmentation of touching cell nuclei using gradient flow tracking, in press, Journal of Microscopy. 2007. 4. Tianming Liu, J Lu, Y Wang, William A Campbell, Ling Huang, J Zhu, Weiming Xia, Stephen Wong. Computerized Image Analysis for Quantitative Neuronal Phenotyping in Zebrafish. Journal of Neuroscience Methods. 153(2):190-202. 2006. 5. William A. Campbell, Henrik Zetterberg, Stephanie Baulac, Tianming Liu, Stephen T. C. Wong, Tao Zhong, Weiming Xia. Zebrafish lacking Alzheimer presenilin enhancer 2 (Pen-2) demonstrate excessive p53-dependent apoptosis and neuronal loss. Journal of Neurochemistry. 96:1423-40. 2006.
Other information
microscopy, segmentation, zebrafish, pipeline
IATR listing last updated
24 Aug 2007