CBI Platform

CBI Platform

Introduction

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 NeuroDiscovery Center, formerly known as the HCNR (Harvard Center for Neurodegeneration and Repair), Harvard Medical School (see http://www.neurodiscovery.harvard.edu/). 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.

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 distributed under the attached license. See http://www.cbi-platform.net/license.htm .

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.

Software Information

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.

Overall design: Tianming Liu, Stephen Wong

Developers: Jingxin Nie, Xiao Wu, Dexing Chen, Tianming Liu

Algorithms and pipeline construction: Gang Li, Jingxin Nie

Documentation: Tianming Liu, Jingxin Nie, Kaiming Li, Dagem Mammo, Stephen Wong

Other contributors: Hai Li, Xintao Hu, Fei Qin, Haifeng Zhao, Hui Yan, Lei Guo, Jianfeng Lu, Ling Huang

Sponsors:

• The Center for Biomedical Informatics, The Methodist Hospital Research Institute, Houston, Texas
• Harvard NeuroDiscovery Center (Formerly known as Harvard Center for Neurodegeneration and Repair), Harvard Medical School, Boston, Massachusetts.

Key Collaborators:
Biological:
Dr. Weiming Xia, Department of Neurology, Harvard Medical School.
http://xialab.bwh.harvard.edu/staff/wxia/ Dr. Jarema Malicki, Department of Ophthalmology, Massachusetts Eye & Ear Infirmary, Harvard Medical School.
http://www.howelaboratory.harvard.edu/malicki.htm Dr. Scott Holley, Department of Molecular, Cellular and Developmental Biology, Yale University.
http://www.biology.yale.edu/facultystaff/holley.html