1. Summary

We need to develop many tools in bioimage informatics to establish workflows for data analysis. This page releases some of the tools we have developed for mouse project and zebrafish project.

2. Mouse Project

Annotation ROI 3D

Software for making annotations on 3D slice images, developed as a plug-in for ImageJ. It can assign an ID for each region extracted by image processing, give annotation for each ID using a checkbox and a textbox, and allow input and output of annotations in XML format. It can be downloaded from annotationRoi3D - GitHub as open source software. Moreover, Annotation ROI 3D Documentation Wiki offers detailed information about installation and documents.

Developed by William Grimes.

MINC Tool Kit

MINC Tool Kit was originally developed by McConnell Brain Imaging Center, and we can use it for the registration of micro-CT images of the mouse. Software code is distributed from the website, but installation is not easy, so we made a Ubuntu virtual machine with MINC Tool kit installed, so that a user can just download it and run.

• How to install the tool
  • Ubuntu.vmx - 1.8KB
  • Ubuntu.vmdk - 17GB
• How to use command-line scripts
• How to use a GUI tool we developed

Developed by Kitti Koonsanit.

3. Zebrafish Project