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The ZFIQ (Zebrafish Image Quantitator) 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.
The ZFIQ can also be used as a platform for integrating and exchange data, algorithms and ideas among zebrafish scientists, developmental biologists, and biomedical researchers.
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.
This version of CBI_Platform( Version 1.0) can only be installed on a windows machine, and the OS should be Windows 2000 or later. To install CBI_Platform, you need to download it first, CBI_Platform is easy to install, like most windows software you have seen. Please read and agree the license
before installation.
Click here for ZFIQ download page: http://www.cbi-tmhs.org/ZFIQ/download.htm
Sponsors:
The Center for Bioengineering and Informatics, The Methodist Hospital Research Institute, Houston, Texas.
Harvard NeuroDiscovery Center(Formally known as Harvard Center for Neurodegeneration and Repair), Harvard Medical School, Boston, Massachusetts.
PI: Professor Stephen Wong
References:
1. Tianming Liu. A quantitative zebrafish phenotyping tool for developmental biology and disease modeling. IEEE Signal and Processing Magazine. 24(1):126-129. 2007.
2. Li G, Liu T, Tarokh A, Nie J, Guo L, Mara A, Holley S, Wong ST. 3D cell nuclei segmentation based on gradient flow tracking. BMC Cell Biol. 2007 Sep 4;8:40.
3. Li G, Liu T, Nie J, Guo L, Malicki J, Mara A, Holley SA, Xia W, Wong ST. Detection of Blob Objects in Microscopic Zebrafish Images Based on Gradient Vector Diffusion. Cytometry A. 2007 Oct;71(10):835-45.
4. Li G, Liu T, Nie J, Guo L, Chen J, Zhu J, Xia W, Mara A, Holley S, Wong ST. Segmentation of touching cell nuclei using gradient flow tracking.J Microsc. 2008 Jul;231(Pt 1):47-58.
5. 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.
6. 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.
7.Tianming Liu, Gang Li, Jingxin Nie, Ashley Tarokh, Xiaobo Zhou, Lei Guo, Jarema Malicki, Weiming Xia. An Automated Cell Detection Method for Quantitative Neuronal Cell Fate Determination in Zebrafish. Neuroinformatics, accepted for publish, 2007.
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