Collaborators and Associated Institutions

Texas Advanced Computing Center (TACC)  TACC designs and operates some of the world's most powerful computing resources. The center's mission is to enable discoveries that advance science and society through the application of advanced computing technologies. The TACC User Portal is the central hub for all things related to using TACC systems.

Salk Institute  The Salk Institute embodies Jonas Salk’s mission to dare to make dreams into reality. We explore the very foundations of life, seeking new realities in neuroscience, genetics, immunology and more. 


MCell  Modeling environment especially developed for 3DEM and used in several Harris Lab publications. CellBlender is an addon for Blender that allows users to create computational cell biology models for use in MCell.

FIJI  Fiji is a distribution of ImageJ bundled with plugins for scientific image analysis.

TrakEM2  TrakEM2 is a FIJI (ImageJ) plugin for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation.

NeuroMorph  NeuroMorph is a toolset designed to import, analyze, and visualize mesh models in Blender. It has been developed specifically for the morphological analysis of 3D objects derived from serial electron microscopy images of brain tissue.

IMOD and SerialEM (for EM tomography)  SerialEM is a program that facilitates image acquisition from FEI and JEOL electron microscopes, including tilt series for electron tomography. IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.

Neuroinformatics Sites

The Neuroinformatics Site  European Union neuroinformatics project coordinated by Eric De Schutter.

WORMATLAS  The database of the neuroanatomy of the nematode C. elegans created by Zeynep Altun and David Hall. This website features many fabulous drawings and micrographs of C. elegans anatomy.

Neuron and Cell Biology Labs

Allen Institute for Brain Science Their mission is to accelerate the understanding of how the human brain works in health and disease. Using a big science approach, they generate useful public resources, drive technological and analytical advances, and discover fundamental brain properties through integration of experiments, modeling, and theory.

Laboratory of Retinal Microcircuitry  3D reconstructions of neurons from the retina. Whole dendritic arbors and cell bodies are reconstructed from ultrathin serial sections.

EM3D  The website of Dr. U. J. McMahan, Professor of Neurobiology and of Structural Biology at Stanford University School of Medicine.  EM3D is a software application designed to facilitate the analysis and visualization of electron microscope (EM) tomography data by cellular and molecular biologists. Such data are collected as a tilt series, a sequence of 2D electron micrographs taken at many tilt angles with respect to the electron beam.

Cell Image Library (National Center for Microscopy and Imaging Research, UCSD)  The Cell Image Library is a freely accessible, easy-to-search, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. The purpose of this database is to advance research, education, and training, with the ultimate goal of improving human health.”

Neuroscience Education  A public information initiative of The Kavli Foundation, the Gatsby Charitable Foundation, and the Society for Neuroscience, overseen by an editorial board of leading neuroscientists from around the world. shares the stories of scientific discovery and the knowledge they reveal.

Dr. Eric Chudler's Homepage  Eric has compiled a huge list of links related to neuroscience and created many pages of general interest. For example:

  • Neuroscience Education  Pages and pages about all aspects of the brain and neuroscience with hundreds of links to on-line articles and other neuroscience web sites.
  • Neuroscience for Kids  Lots of educational material about the nervous system. A good resource for both teachers and students.
  • Brain Facts  Want to know the weight of the brain of a human? whale? elephant? platypus? Or the number of neurons in the brain? Or the composition of the brain? It's all in this concise list of facts about the nervous system.

Whole Brain Anatomy

Digital Anatomist Project  Dissect a digital recreation of the human nervous system using 3D reconstructions created by the University of Washington Health Science Center for Educational Resources.

The Whole Brain Atlas  An atlas of the human brain in health and disease as imaged using tomographic imaging modalities, including magnetic resonance (MR), roentgen-ray (CT), and nuclear medicine. The site includes over 13,000 brain images from 32 cases. 

Comparative Mammalian Brain Collections  The combined collections of the University of Wisconsin, Michigan State and the National Museum of Health and Medicine are the basis for this website, featuring photographs of brains of over 100 different species of mammals representing 17 mammalian orders. In addition, the curators are capable of providing stained, serial sections of many of the species in the collections. For example, Dr. Wally Welker provided us with sections of the California sea lion brain from which we obtained this reconstruction.