Software Downloads

NCMIR develops post data-collection computer-aided image analysis resources and computer graphics tools. Computational tools available for download include applications for electron microscopic tomography, large-field light microscopy, visualization, file format conversion, specialized plug-ins, and grid computing tools. These software tools are used for computer graphics and image processing to delineate biological structures, including the derivation of contours, their editing, exploration of semi-automatic contouring, and volumetric contouring. NCMIR software can be obtained without Scientific Advisory Board approval. If you have questions or need additional information call (858) 534-0276

To obtain these software packages, please consent to the Software Download Agreement.

Electron Microscopic Tomography

		Dend Dend is an interactive program for resectioning and deriving measurements from contoured structures. It creates structural measurements obtaining lengths, surfaces, and volumes from volume data. Investigation of 3D structures and communication to others are greatly facilitated by this computer-based visualization. Requirements Dend: X Window and OpenGL

		Fido Fido is an interactive, graphic, fiducial marking software for placing, editing, and tracking fiducial marks on images in a tomography tilt series. You can also use this tool to view and crop the tilt series. Requirements XFido: X Window and OpenGL JFido: Java and Java Web Start

		Xvoxtrace Xvoxtrace enables volume segmentation of tomographic data using manual tracing. This program allows the researcher to outline features on individual planes of the volume while being guided by simultaneous views of the tracing displayed on a volume rendering or tilt-series. Traced contours can be viewed using XDend or used to generate surfaces for viewing in Synu. Requirements Xvoxtrace: OpenGL, X windows, and Linux platforms

Mosaic Creation Plugins for ImageJ

ImageJ
The set of ImageJ plug-ins included in this distribution form the mosaic processing software we use at NCMIR to process our large-scale brain maps and mosaics. The reason the software exists as ImageJ plug-ins is largely due to legacy and uses very little of the ImageJ functionality. Instead, the plug-ins makes substantial use of the Java Advanced Imaging and Image I/O libraries for most of the image processing and file I/O. Consequently, image files created with the mosaic processing pipeline generally are not fully compatible with the built-in functionality of ImageJ.

For more info, go to ImageJ Page.

Visualization

		Btrack Btrack analyzes and graphs time-lapse imaging data as acquired by a Bio-Rad confocal microscope, for experiments using nonratiometric fluorescent indicator dyes. Btrack can accommodate changes in the positions of imaged cells/tissue regions and can be used for analyzing an unlimited number of areas (cells/tissue regions) in an imaged field. Requirements SGI IRIX and Iris GL

		JViewer JViewer is a 3D viewer written in Java and Java 3D and launchable via the web. It has been integrated into the BIRN Portal, the Telescience Portal, and the Cell Centered Database (CCDB). It can currently view Synu polygon mesh, Voxtrace contours, and Microbrightfield's Neurolucida V3 ASCII file formats. Requirements Java and Java 3D


		Synuview/OpenSynu Synuview/OpenSynu allows for interactive investigation of 3D volumes and the production of high-quality 3D images of the data. Synuview/OpenSynu works with polygon meshes, stacks of contour lines, or 3D volumes from confocal Z-series, tomography, or simulations. Requirements X Window and OpenGL

File Format Converters

Requirements
Many of these are command line applications for various platforms.

Photoshop plug-in — works on various versions of photoshop
Imodinfo — gets information on an IMOD file
an2pgm — converts an Analyze volume into Portable Gray Map
an2suprim — converts an Analyze volume into SUPRIM [Documentation PDF]
imodtoanalyze — converts IMOD to Analyze 7.5 format [Documentation PDF]
imodtosuprim — converts IMOD to SUPRIM [Documentation PDF]
lstac — takes a stack of SUPRIM files and creates a SUPRIM volume [Documentation PDF]
mrcconv — converts to and from MRC, SUPRIM, IMOD, and Analyze [Documentation PDF]
mrcinfo — gets information on an MRC file [Documentation PDF]
mrctoanalyze — converts MRC to Analyze 7.5 format [Documentation PDF]
mrctomrc — converts between MRC variants [Documentation PDF]
mrctosuprim — converts MRC to SUPRIM [Documentation PDF]
pgm2an — converts a stack of Portable Gray Map files to Analyze 7.5 format [Documentation PDF]
slime — Steve Lamont's Image Editor
suprim2pgm — converts SUPRIM files to Portable Gray Map [Documentation PDF]
suprimhist — calculates histogram and image statistics for SUPRIM files [Documentation PDF]
suprimtomrc — converts SUPRIM to MRC [Documentation PDF]
suprimtotiff — converts SUPRIM to TIFF [Documentation PDF]
supvol2an — converts a SUPRIM volume file to Analyze 7.5 format [Documentation PDF]
tifftoan — converts a TIFF stack or series of files to Analyze 7.5 format
tifftosuprim — converts a TIFF stack or series of files to SUPRIM format [Documentation PDF]

Generalized Grid Tools

		Telescience Distribution Package The distribution package contains Perl modules and libraries that can be used to build a grid portal very quickly. The package provides a generic HTML-based data grid browser and example pages to launch grid-based jobs. Requirements Gridport Toolkit 2.x, Globus2.x, GSI-enabled SRB client tools

		Data Grid Browser The Data Grid Browser is a JSR168-compliant interface to browse a data grid. Requirements JSR16- compliant portal framework (i.e., Gridsphere)

		Java Grid Interface The JGI is a wrapper application that allows non-grid enabled applications to access data stored on a data grid. Requirements Java 1.4.x