| Electron
Microscopic Tomography |
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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 |
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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
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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 |
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| Large-Field Light
Microscopy |
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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
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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. |
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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. |
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Combine RTS2000
Combine RTS2000 performs the actual auto-alignment
and the composition of images to create the
mosaic. |
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| Visualization |
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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 |
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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 |
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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 |
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| File Format Converters |
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Requirements
Many of these are command line applications
for various platforms. |
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Photoshop plug-in —
works on various
versions of photoshop |
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Imodinfo
— gets information on an IMOD
file |
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an2pgm
— converts an Analyze volume
into Portable Gray Map |
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an2suprim
— converts an Analyze volume
into SUPRIM
[Documentation PDF] |
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imodtoanalyze
— converts IMOD to Analyze 7.5
format
[Documentation PDF]
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imodtosuprim
— converts IMOD to SUPRIM
[Documentation PDF]
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lstac —
takes a stack of SUPRIM files and creates
a SUPRIM volume
[Documentation PDF]
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mrcconv
— converts to and from MRC, SUPRIM,
IMOD, and Analyze
[Documentation PDF]
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mrcinfo
— gets information on an MRC
file
[Documentation PDF]
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mrctoanalyze
— converts MRC to Analyze 7.5
format
[Documentation PDF]
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mrctomrc
— converts between MRC variants
[Documentation PDF]
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mrctosuprim
— converts MRC to SUPRIM
[Documentation PDF]
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pgm2an
— converts a stack of Portable
Gray Map files to Analyze 7.5 format
[Documentation PDF]
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slime
— Steve Lamont's Image Editor |
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suprim2pgm
— converts SUPRIM files to Portable
Gray Map
[Documentation PDF]
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suprimhist
— calculates histogram and image
statistics for SUPRIM files
[Documentation PDF]
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suprimtomrc
— converts SUPRIM to MRC
[Documentation PDF]
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suprimtotiff
— converts SUPRIM to TIFF
[Documentation PDF]
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supvol2an
— converts a SUPRIM volume file
to Analyze 7.5 format
[Documentation PDF]
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tifftoan
— converts a TIFF stack or series
of files to Analyze 7.5 format |
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tifftosuprim
— converts a TIFF stack or series
of files to SUPRIM format
[Documentation PDF]
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| Generalized Grid
Tools |
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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 |
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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) |
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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
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