Software Downloads

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

Jinx
Jinx is a Java application which enables volume segmentation of tomographic data using manual tracing. This program allows the researcher to outline features on individual planes of the volume.
Jinx is designed to be a cross-platform replacement for Xvoxtrace,
which is at "end of life" and no longer actively supported.

Requirements: Java 1.5 (aka Java 2) or greater, 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

Montaging Plug-ins
The following montaging plug-ins are all part of a series of steps that are required to complete a mosaic.

Requirements
Image J, Java 1.4.x, Java Advanced Imaging Toolkit, JadeDisplay

Montage RTS2000
Montage RTS2000 opens up the *.img files saved from a 2-photon scope and performs the necessary pre-processing. It reads information about the montage saved into the header section of the file, z-projects the data as needed, separates the data into X-Y chunks, and saves the chunks into *.tif format.

Manual Align RTS2000
Montage RTS2000 allows a user to adjust the alignment of two adjacent images. This allows the user to correct for any misalignment that may occur during auto-alignment step in the overall process and also serves as a "bootstrap" to get the images in approximately the right place.

Combine RTS2000
Combine RTS2000 performs the actual auto-alignment and the composition of images to create the mosaic.

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

Jinx
Jinx is a Java application which, in theory at least, should run on most modern computers and operating systems with little or no need for installation or configuration. When you click on the link to run Jinx, you download a small file which your web browser should automatically recognize and cause the appropriate Java "jar" files to be downloaded through Java Web Start. Using this mechanism ensures that you will always be using the most current and up to date version of Jinx without having to keep up with patches, versions, or complicated downloads.

Scalable Adaptive Graphical Environment (SAGE) for Windows 32-bit
SAGE is a graphics streaming architecture for supporting high-resolution, scalable and collaborative scientific visualization environments. It is primarily designed to be run as a thin middleware on cluster driven tile-displays. It allows users to treat the high-resolution distributed displays as one contiguous desktop where users can move/resize application windows. SAGE is network centric and the applications running on these displays need not run locally. The applications can be run on remote machines or clusters and can stream their pixel framebuffers to SAGE enabled tile-displays.

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

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