Data from the CCDB can be visualized and analyzed using a variety of tools. Computational tools such as XVoxtrace, and SynuView are available through the Software Downloads section of the NCMIR website. Future versions of this CCDB section will have these and additional tools available for Download. In the interim, use the NCMIR Downloads section.
ImageJ - Image processing and analysis in Java. Can be used to open formats by loading appropriate plug ins.
Biorad Reader Plug-In - Uses ImageJ to read Biorad PIC format. Opens a Biorad z-series of images as a stack. The width, height and number of images are extracted from the first 3 16-bit word in the 76 byte header and the spatial calibration is extracted from the ASCII "notes" at the end of the file. Use Image/Show Info to display all the "notes".
Jinx - Java-based tool for segmentation of
3D volume data. Jinx may be used to view volume data in Analyze 7.5 format
and segmentations produced using Xvoxtrace. Jinx is the replacement
program for Xvoxtrace.
Load/Save Analyze Files - Plug-ins to load and save images in Analyze format with ImageJ.
Neurolucida - A commercial package used to view tree structures.
NCMIR File Format Converters - Javascript and Java required for use.
Massachusetts General Hospital Image Analysis Tools Registry - Visualization and analysis tools available. There is no charge for the tools, but registration is required.
IMOD - A set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. Many of the datasets in CCDB were created and can be viewed and analyzed in IMOD.
