Confocal Microscopy Visualization

This page is a collection of pointers to information that Russ Taylor found while looking for confocal microscopy visualization techniques. A related page describing computational optical sectioning microscopy is found here. Some other links related to commercial hardware and software packages for both Confocal and COSM is found here.

Within NIH/NCRR Centers

Ultrafast Optical Processes Laboratory at the University of Pennsylvania. Phase-controlled infrared pulses, time-correlated single-photon counting, transient spectroscopy, photon echoes, two-photon absorption, and time-resolved confocal microscopy. Inverted confocal microscope with time-correlated single-photon counting. Aiming at studying conformation changes in proteins and peptide folding.

National Center for Microscopy and Imaging Research at UCSD. Computer-aided techniques for deriving 3-D information from 3-D light and electron microscopy: merging these two data sets (confocal and IVEM) from the same sample. Reconstruction algorithms running on SDSC machines. Biorad MRC 1024 and custom-built video-rate 2-photon microscope. A research project in visualizing confocal microscope data (including flythroughs) at SDSC can be found at

Developmental Resource for Biophysical Imaging and Opto-Electronics at Cornell. They have four laser scanning microscopes with mode-locked lasers to provide 100fs pulses at 80 MHz with wavelengths tunable from 690nm to 1000 nm for multiphoton imaging of UV and visible adsorbing fluorophores. 3-D resolved micoroscopic imaging of fluorescence at single-molecule sensitivity in and on cells.

Laser Microbeam and Medical Program at UC Irvine. Confocal ablation trapping system (CATS) integrates trapping and cutting beams into a Zeiss laser scanning confocal microscope. Applications: Tumor diagnosis in breast, brain, and cervix.

NIH/NCRRs with work related to confocal microscopy

Center for Fluorescence Spectroscopy at the University of Maryland, Baltimore. Time-domain and frequency-domain measurement and analysis of fluorescence, including Fluorescence lifetime imaging microscopy (FLIM).

Laboratory for Fluorescence Dynamics at UIUC. Studies fluorescence correlation spectroscopy (FCS). Has time-resolved and steady-state fluorescence instrumentation. Has capability to image in-plane and 3D, with particle tracking; software for image analysis such as photon-counting histograms.

Laser Biomedical Research Center at MIT. Developing techniques for 3-D optical imaging of biological tissue.

Non-NCRR Centers

Optical Microscopy Facility at the Herbert Irving Comprehensive Cancer Center. One-photon Laser Scanning Microscope: A Zeiss LSM 410 scanning laser confocal system is mounted on a Zeiss Axiovert 100 TV inverted fluorescence microscope equipped for fluorescence and transmitted-light imaging. An argon-krypton laser and three photomultiplier detectors offer the ability to image up to three fluorophores simultaneously. The software for confocal image analysis offers three-dimensional reconstruction, stereoscopic volume display, time-lapse imaging, ratio imaging, photobleaching (FRAP), quantifying co localization, and morphometry.

Laser scanning confocal microscope at the Imaging Technology Group at the Beckman Institute at the University of Illinois, Urbana-Champaign. This page hints at programs that they have that converts the proprietary .PIC format from the Zeiss instrument to and from a TIFF format.

Owen Price and Robert Zucker have a web page that describes how to analyze data from a multi-spectral image, where there is different distortion based on wavelength.

Programs for display and analysis of confocal data sets

The 3DSlicer program ( is a VTK-based program. The 3D Slicer is freely available, open-source software for visualization, registration, segmentation, and quantification of medical data. Development of the Slicer is an ongoing collaboration between the MIT Artificial Intelligence Lab and the Surgical Planning Lab at Brigham & Women's Hospital, an affiliate of Harvard Medical School. has a list of software available for the 3D reconstruction of MRI, CT, confocal, and serial-section data for medical/life sciences imaging. Some links are to packages that are quite old (Irix GL).

The most promising free ones appear from a quick glance to be Montage, which is a serial-slice reconstruction tool; ROSS, which is another reconstruction tool; XCOSM, which was an X-windows interface for two COSM (computational optical sectioning microscopy) programs that remove out-of-focus light in volume data collected plane by plane.

Commercial systems include CELLScan, which assigns photons from through-focus or confocal data sets back to the proper slices; AVS Express, which is a general-purpose visualization toolkit.

Another commercial system is the 3D Construction plug-in for Image-Pro, made by MediaCybernetics. There is a web page for this.

There is another list of software that is available at, which is a list of lots of microscope software packages. It also lists image galleries, movies, and places that do 3D imaging.

Random web hits to relevant papers and work

There is a page of links to confocal sites on the web with images and animations maintained by the Lance Ladic at the CS department at UBC. I've copied the table from the page here in case it goes away in the future.

The PRISM group at ASU has a paper describing a system they developed for the display of multicolor-laser confocal data.

The American Museum of Natural History has video of a pollen grain reconstructed from confocal data.

Wim de Leeuw, Robert Van Liere, et. al. have a paper in Visualization 2000, "Visualization of Time Dependent Confocal Microscopy Data" that shows microtubule dynamics. Also, in Visualizaton 2001 they have a paper "Chromatin Decondensation: a case Study of Tracking Features in Confocal Data."

A paper from the PRISM group at the University of Arizona by Razdan, Patel, Farin, and Capco, entitled "Volume Visualization of Multicolor Laser Confocal Microscope Data."

An IEEE Visualization 1996 paper by Saka, Vicker, and Plath entitled, "Case Study: Visualization of Laser Confocal Microscopy Datasets."

"Feature Extraction of Chomosomes from 3-D Confocal Microscope Images" by Matthew J. Kyan and Ling Guan from IEEE Transactions on Biomedical Engineering, Vol 48, No 11, Nov 2001. Pages 1306-1318.

Descriptions of how Confocal Microscopy works

Notable papers and such sent by Rich

Paper comparing confocal scanning microscope and COSM on the same data set can be found here.