Software Downloads
There are 29 files, weighing 786.8 MiB with 42,180 hits in total.
Displaying 1 to 29 of 29 files.
ImageSurfer
ImageSurfer 2.0.2 Mac OS X 64-bit
» 53.9 MiB - 54 hits - November 16, 2011
ImageSurfer 2.0.2 Windows 64-bit
» 60.5 MiB - 111 hits - November 4, 2011
ImageSurfer 1.27
» 40.9 MiB - 1,495 hits - May 4, 2010
Image Surfer v.1.27.
ImageSurfer is a software application used to view stacks of grayscale images, taken from a confocal microscope, as volumes. The user may choose different views--each offering a different interpretation of the data. In turn, the user may interact with the data as a three-dimensional volume or surface.
See the ImageSurfer web site for more instructions on downloading and using the software. A tutorial is available online.
ImageSurferInstaller v.1.24JRE.msi
» 40.9 MiB - 4,829 hits - February 5, 2009
Version 1.24 of ImageSurfer.
Video Spot Tracker
setup_video_spot_tracker_v06_04.exe
» 10.1 MiB - 1,220 hits - October 11, 2009
Video Spot Tracker.
The Video Spot Tracker program is used to track the motion of one or more spots in a Microsoft DirectShow-compatible video file, from a Microsoft DirectShow-compatible camera, from a Roper Scientific camera, or from a DiagInc SPOT camera.
See the Video Spot Tracker manual for more information about the program. There are four tutorials available online:
ImageTracker
ImageTracker
» 7.5 MiB - 4,236 hits - October 21, 2008
ImageTracker is a motion analysis application specifically designed for video microscopy. ImageTracker can stabilize image sequences with respect to moving objects, remove the effect of stationary components from bright field images, and compute and visualize dense displacement fields that explain motion in image sequences (optical flow). New in ImageTracker 3.0 is the ability to apply numerous image filters as well as an improved multi-resolution optical flow implementation.
See the ImageTracker web page for more information, including a manual. There are two tutorials available online: Image Stabilization and Removal of Stationary Image Components
Microscope Simulator
Microscope Simulator 2.0.0 for Intel MacOS X 10.5
» 53.4 MiB - 1,131 hits - August 6, 2010
Microscope Simulator version 2.0.0 enables a scientist to simulate what a given 3D scene should look like under a fluorescence microscope. 3D scenes can be constructed from primitives or imported files in VTK, OBJ, or PLY format. Once a 3D model has been created, you can provide the point spread function (PSF) for a given fluorescence microscope and view simulated fluorescence images.
Version 2.0.0 of the Microscope Simulator features a more intuitive user interface and a new multi-fluorophore optimization algorithm in the FluoroSim module.
For AFM simulation, please use an earlier version (1.3.1 and earlier) of Microscope Simulator.
Microscope Simulator 2.0.0 for Windows XP/7
» 14.1 MiB - 1,180 hits - August 6, 2010
Microscope Simulator 1.3.1 for Windows XP/7
» 42.6 MiB - 1,296 hits - September 17, 2009
The Microscope Simulator enables a scientist to simulate what a given 3D scene should look like under a fluorescence microscope or an atomic force microscope (AFM). 3D scenes can be constructed from primitives or imported files in VTK, OBJ, PLY, or UNCA format. Once a 3D model has been created, you can provide the point spread function (PSF) for a given fluorescence microscope and view simulated fluorescence images. In addition, you can specify the parameters of a simple AFM tip model and quicky generate a simulated AFM surface scan.
See the Microscope Simulator web page for more instructions on using the program. A tutorial is available online.
Previous versions are available below:
Microscope Simulator 1.3.0 for Windows XP/7
» 40.1 MiB - 1,816 hits - June 5, 2009
Version 1.3.0 of the Microscope Simulator software.
Microscope Simulator 1.2.2 for Windows XP/7
» 43.4 MiB - 854 hits - September 1, 2008
Version 1.2.2 of the Microscope Simulator software.
Video Optimizer
setup_cismm_video_optimizer_02_00_2.exe
» 7.7 MiB - 1,973 hits - August 12, 2009
The CISMM Video Optimizer provides contrast and gain control, cropping, and point-based image stabilization on stacks of TIFF files and video files. It also enables simplified background subtraction and the accumulation of minimum, maximum, and average video frames.
Available online are a manual and two tutorials: Actin Motility and Mitotic-spindle Dynamics.
VRPN Log to Matlab
vrpnLogToMatlabInstaller_05_00.exe
» 10.4 MiB - 2,397 hits - July 27, 2010
This utility converts VRPN log files from 3DFM-related programs into a format readable by MATLAB.
Template-Based Matching
setup_template_based_matching_v01_05_1.exe
» 4.9 MiB - 2,425 hits - October 28, 2010
The CISMM Template-Based Matching program is designed to locate and identify objects within Scanned-Probe Microscope images and produce a file of descriptive statistics about these objects.
A manual and a tutorial are available online.
Plot Extractor
setup_CISMM_plot_extractor_02_05.exe
» 3.4 MiB - 2,563 hits - December 10, 2008
The Plot Extractor program is used to extract plot data from a TIFF image of a plot or series of plots. The data is saved in comma-separated values (.csv) format, which is readible by a number of programs including Excel and Matlab. The program currently runs only on Windows.
Edge Detector 1D
edge_detector_1d_v01_02.zip
» 99.5 KiB - 2,718 hits - October 29, 2008
Edge Detector 1D is a collection of Matlab scripts that performs multi-scale edge detection on one-dimensional data. The download includes documentation on how to use the program.
Clarity
Clarity Deconvolution Library 1.0
» 137.3 KiB - 2,895 hits - December 14, 2008
Clarity is an open-source C/C++ library implementing many of the common deconvolution algorithms used in fluorescence microscopy. It is designed specifically for processing 3D images generated from optical sectioning. Clarity uses multithreaded algorithms to make full use of all the cores on modern multi-core computer systems. For even greater performance, the deconvolution algorithms can optionally run on commodity graphics processing units that feature hundreds of computing cores. Support for acceleration on graphics processing units is currently available on NVIDIA graphics cards.
The latest source code is available on GitHub.
WebSlinger
webslinger-4.0.1 for Intel Mac
» 52.5 KiB - 18 hits - October 8, 2011
setup_webslinger.4.0.1.msi
» 494.5 KiB - 2,458 hits - March 7, 2009
WebSlinger v. 4.0.0.
The WebSlinger program is used to simulate the deformation of a 2D web of masses connected by springs. The springs can be linear or nonlinear (with specified strain/force curves). The initial rest length and spring constant can be calculated based on the initial positions of the points and an initial strain estimate.
You can interact with the simulation by pulling on individual masses with the mouse. You can also set trajectories for one or more masses and compute the response of the other masses.
Network Extractor
Network Extractor 1.0.0 for Intel MacOS X 10.5
» 51.8 MiB - 1,043 hits - August 17, 2010
Network Extractor is a program for segmenting and collecting statistics on fibrous objects in 3D images. It has been developed with the specific target of fibrin network images in mind, but can be applied to images of any kind of fibrous object such as collagen or actin networks, for example.
A tutorial for the program is available.
Network Extractor 1.0.0 for Windows XP/7
» 15.7 MiB - 1,051 hits - August 17, 2010
Mystery of the Sick Puppy
sick-puppy.exe
» 123.8 MiB - 1,088 hits - January 15, 2003
Installer for "The Mystery of the Sick Puppy", an instructional module to enhance knowledge about viruses, their structure, and how they replicate.
PSF Estimator
PSF Estimator 1.0.0 for Windows XP/7
» 15.5 MiB - 738 hits - October 14, 2010
PSF Estimator 1.0.0 for Intel MacOS X 10.5
» 54.9 MiB - 973 hits - October 14, 2010
PSF Estimator is a program for fitting mathematical models of point-spread functions from microscopes to images of fluorescent beads with diameters below the resolution limit imposed by diffraction. Currently, only PSFs from widefield fluorescence microscopes are supported.
Simple Stereo
setup_stereo_spin_v02.02.exe
» 7.5 MiB - 704 hits - October 17, 2010
The Stereo Spin program is used to display stereo images from a spinning-loop video, making it easy to display stereo content from scientific visualizations or animations that were not originally rendered in stereo. It drives OpenGL stereo hardware if it is available. It can also drive cross-eyed stereo on any computer.
PreAnalysis
preanalysis-1-0.exe
» 40.0 MiB - 521 hits - November 9, 2010
The PreAnalysis application will open a vrpn tracker log or a live vrpn tracker connection in order to calculate and display a mean-squared-displacement (MSD) plot.
Chromatin Cutter
ChromatinCutter 1.0.0 Mac OS X Universal
» 12.9 MiB - 36 hits - October 13, 2011
CISMM_Chromatin_Cutter
» 21.3 MiB - 297 hits - May 19, 2011
This program simulates the distribution of DNA in a gel electrophoresis study of Yeast chromatin cut by enzymes. It lets you specify the fraction of nucleosomes that are unwrapped (wrapped ones have inaccessible DNA). It lets you specify the variance in the distribution of nucleosomes around their mean distance. It lets you specify the number of cuts per unit length (enzyme concentration). It plots the effects of these on the log number of base pairs, which matches the gel electrophoresis mass distribution. This provides a way to investigate whether features seen in the distribution are caused by nucleosome unwrapping or by nucleosome position variation.
Camera Calibration
camera_calibration_2_0_1.zip
» 8.9 MiB - 60 hits - August 5, 2011
Camera-calibration program brought to you jointly by CISMM.org and Megawatt Solar, Inc. This tool lets you print out a 2D color pattern that uses red and green to form a grid and blue to identify the grid, so that by selecting a few boundary points and thresholds you can automatically determine the camera's intrinsic and extrinsic parameters. It uses Tsai's method (source code included) to do the calculations once it has selected the points.