Contact Joe Hsiao at for software issues.

There are 48 files, weighing 1.9 GiB with 140,592 hits in total.

Displaying 1 to 48 of 48 files.


  ImageSurfer 2.5.2 Windows 64bit
» 39.5 MiB - 4,332 hits - September 2, 2014
Tutorials are available at here.

  ImageSurfer 2.5.2 Linux 64bit
» 190.7 MiB - 195 hits - September 2, 2014

  ImageSurfer 2.5.2 Mac 64bit
» 89.1 MiB - 1,331 hits - September 2, 2014

  ImageSurfer 1.27 Windows 32bit
» 40.9 MiB - 37,831 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 - 6,180 hits - February 5, 2009

Version 1.24 of ImageSurfer.

Video Spot Tracker

» 25.9 MiB - 1,016 hits - October 28, 2013
Fro Mac OSX 10.5 or newer

» 22.5 MiB - 1,827 hits - September 2, 2013

Video Spot Tracker.

The Video Spot Tracker program is used to track the motion of one or more spots in a set of image files, a video file, from a Microsoft DirectShow-compatible camera, or from some scientific cameras.

See the Video Spot Tracker manual for more information about the program. There are four tutorials available online:


  ImageTracker source code
» 21.0 MiB - 315 hits - August 19, 2013

» 7.5 MiB - 5,651 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 2.3.0 for Windows XP/7 64-bit
» 25.7 MiB - 563 hits - July 26, 2013

Microscope Simulator 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. Check out the tutorial.

The Microscope Simulator features an intuitive user interface and a 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 2.2.1 for Intel MacOS X 10.6
» 52.4 MiB - 497 hits - January 23, 2013

  Microscope Simulator 2.2.1 for Windows XP/7 64-bit
» 25.1 MiB - 618 hits - January 23, 2013

  Microscope Simulator 2.2.1 for Windows XP/7 32-bit
» 21.4 MiB - 675 hits - January 23, 2013

  Microscope Simulator 1.3.1 for Windows XP/7
» 42.6 MiB - 2,161 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:

Video Optimizer

» 13.7 MiB - 1,323 hits - April 22, 2013

» 16.5 MiB - 1,029 hits - April 20, 2012

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

» 10.4 MiB - 35,450 hits - July 27, 2010

This utility converts VRPN log files from 3DFM-related programs into a format readable by MATLAB.

Template-Based Matching

» 4.9 MiB - 3,294 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

» 3.4 MiB - 3,404 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.

A manual and a tutorial are available online.

Edge Detector 1D
» 99.5 KiB - 4,591 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.

A manual and a tutorial are available online.


  Clarity Deconvolution Library 1.0
» 137.3 KiB - 3,638 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.

A manual is available online.

The latest source code is available on GitHub.


  WebSlinger source code
» 5.0 MiB - 100 hits - February 17, 2014

  webslinger-4.0.1 for Intel Mac
» 63.7 KiB - 798 hits - May 3, 2012

» 494.5 KiB - 3,431 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 Windows XP/7 (64bit)
» 34.3 MiB - 501 hits - July 19, 2013

  Network Extractor 1.0.0 for Intel MacOS X 10.5
» 51.8 MiB - 1,878 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 - 2,074 hits - August 17, 2010

Mystery of the Sick Puppy

» 123.8 MiB - 1,987 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 1.1.0 for Windows 7
» 22.8 MiB - 942 hits - October 19, 2012

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.

Source code is available here.

  PSF Estimator 1.1.0 for Intel MacOS X 10.6
» 44.7 MiB - 518 hits - October 19, 2012

  PSF Estimator 1.0.0 for Windows XP/7
» 15.5 MiB - 1,913 hits - October 14, 2010

  PSF Estimator 1.0.0 for Intel MacOS X 10.5
» 54.9 MiB - 1,710 hits - October 14, 2010

Simple Stereo

» 7.5 MiB - 1,472 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.


» 40.0 MiB - 1,385 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 - 776 hits - October 13, 2011

» 21.3 MiB - 1,400 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
» 6.4 MiB - 348 hits - May 29, 2012
Camera-calibration program brought to you jointly by 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 coplanar method (source code included) to do the calculations once it has selected the points.

Well Layout

» 27.5 MiB - 1,078 hits - April 24, 2012

Well Layout 1.2.1

The Well Layout program lets you describe a 96-well experiment using a graphical user interface.

Layouts (and object in them) can be stored in a persistent Postgres SQL database or they can be stored in CSV-format files on a local hard drive.

Landmark Registration

  LmRegistration Matlab Script
» 2.8 MiB - 530 hits - April 2, 2013

This Matlab tool locates fiducials or markers in images from correlative microscopy and estimates transformations from them to achieve image registration.

The tutorial is here

  Landmark Registration for Windows 64bit (Including Matlab Runtime)
» 178.4 MiB - 394 hits - June 7, 2012
If you don't have Matlab, download this one. Otherwise, you can download Matlab scripts only from below. The tutorial is here

  Landmark Registration for MacOSX 10.7 (Including Matlab Runtime)
» 351.0 MiB - 238 hits - June 7, 2012
If you don't have Matlab, download this one. Otherwise, you can download Matlab scripts only from below. The tutorial is here

Spindle Simulation

» 1.4 MiB - 175 hits - February 12, 2013
Matlab source code and PDF manual for the Spindle Simulation published in the 2013 JCB paper "Pericentric Chromatin Loops Function as a Non-linear Spring in Mitotic Force Balance" with Andrew Stephens as the first author. This is a mechanical model of the behavior of the mitotic spindle of yeast during metaphase.


  BrightPixel v1.0
» 126.7 KiB - 160 hits - August 9, 2013
BrightPixel is a plugin/script to Fiji (Fiji Is Just ImageJ) written in Jython that allows the user to track the movement of multiple fluorescent dots in 3D fluorescence micrograph videos. More abstractly, it tracks the motion of high intensity regions of pixels in a hyperstack opened in Fiji that defines a time series of z-stacked images.


  nanoManipulator server for the Asylum microscope
» 184.0 KiB - 221 hits - December 21, 2013
This is the "External Operations" (XOP) file that provides a network interface for an Asylum scanned-probe microscope so that the nanoManipulator system can connect to it. This system was developed by 3rdTech when it sold the system through 2013. It is now released under the Boost open-source license. To use it, you also need to download the nanoManipulator installer. Contact for the source code.

  nanoManipulator installer
» 9.4 MiB - 206 hits - December 21, 2013
The nanoManipulator is a virtual-reality interface to scanned-probe microscopes. It was licensed to 3rdTech, who sold the system and support through 2013. It is now an open-source tool available free for use, licensed under the Boost software license. This is the installer for the application. Using it also requires installing the Asylum External Operations (XOP) file on an Asylum scanned-probe microscope, or building a network interface for another microscope. Contact for the source code.

Video Averager

  CISMM Video Averager
» 3.6 MiB - 179 hits - April 3, 2014
This installer includes a pair of video utility functions with desktop shortcuts. One of them computes an image that is the average of all frames in a video (or file sequence). The other computes the maximum pixel values across the video. It stores a composite image in the same directory as the files it is run on. You run the scripts by dragging the video file (or one of the images from a sequence) and dropping it onto the desktop shortcut.


  SketchBio Installer
» 187.4 MiB - 172 hits - September 22, 2014
64-bit Windows installer for SketchBio version 0.0.10. See the installation guide for further instructions on how to set up SketchBio on your computer.
» 7.8 MiB - 85 hits - August 1, 2014
SketchBio aims to provide a rapid-to-use and easy-to-learn 3D modeling tool for biologists to enable effective interactive 3D “what if” scenario exploration for the exploration of subcellular structures. This is the source code for SketchBio.