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Download Software

This page contains pointers to software packages that have been developed wholly or in part by the NIH Center for Computer Integrated Systems for Microsopy and Manipulation at the University of North Carolina at Chapel Hill.

ImageSurfer

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 page for more instructions on downloading and using the code.

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. The program currently runs only on Windows, but it uses the portable openGL library for rendering and the portable Tcl/Tk for user interface control.

Version 05.20 available now. See the Video Spot Tracker web page for more instructions on the program.

Download Video Spot Tracker v05.20 here

Download NSRG Runtime v01.13 here.

Fluorescence and Atomic Force Microscope Simulator

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.

Download Microscope Simulator 1.2.1 here.

Plot Extractor

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.

See the Plot Extractor web page for instructions on using the code.

Download Plot Extractor v02.02 here.

Download and install the required NSRG Runtime v01.13 here.

Template-Based Matching

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. To use it, you must have first installed NSRG Runtime.

Download Template-Based Matching v01.04 here.

VRPN Log to Matlab

Download version 03.07 here.

Video Optimizer

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.

Download version 01.13 here.

Download NSRG Runtime v01.13 here.

Edge Detector 1D

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.

Download the Edge Detector zip file here.

See the Edge Detector web page for more information.

ImageTracker

ImageTracker is an application designed to track and measure motion in image sequences.

Download the ImageTracker for Windows installer here.

See the ImageTracker web page for more information.

VRPN

CISMM developed a core library for interfacing with various virtual-reality devices (locally or across a network) that supports trackers from more than six different vendors and more than fourteen button/analog/joystick devices. The library, named the "Virtual Reality Peripheral Network," is written in C++ and has been ported to many variants of Linux and to Windows. There are Java bindings for the remote "user" objects (as opposed to server objects) in development. See the VRPN web page for more information on the library and for instructions on downloading the code.