The Mouse Brain Library
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About MBL

The MBL consists of high-resolution images and databases of brains from many genetically characterized strains of mice. There are numerous uses of the MBL, but our own mission is to systematically map and characterize genes that modulate architecture of the mammalian CNS (for a complete description of our projects refer to our P20 Human Brain Project award: Informatics Center for Mouse Neurogenetics). For example, we want to understand much more about normal genetic variants (normal alleles, not necessarily mutations) that generate differences in cell populations and cell phenotypes in hippocampus, cerebellum, striatum, olfactory bulb, thalamus, and neocortex. For this reason, MBL databases also include detailed information on genomes of many strains of mice (see BXN release 1). The collection now consists of images from approximately 800 brains and numerical data from just over 8000 mice.

You can search the MBL for cases by strain, age, sex, body or brain weight. Images of the slide collection are available at a series of resolutions. The base resolution is 24.5 ± 0.5 µm per pixel in the XY plane with a 150 µm interval between sections (300 µm on each slide, 2 slides per case). Significantly higher resolution images of single sections—4.5 µm/pixel—have been acquired for over a hundred cases marked with a blue "hi-res" button. We are now collecting 1 µm/pixel images for specific parts of the brain—at present, the neocortex, hippocampus, and the dorsal lateral geniculate nucleus. Very high resolution images (<0.2 µm/pixel) are available for C57BL/6J using the iScope, a web-controlled microscope equipped with DIC optics. The quality of images displayed on your monitor will depend on your system, monitor settings, and other software configurations. Macintosh users of Internet Explorer 5: please note that the right side of large JPEG images are often cropped. To circumvent this problem, please use IE4.5 or Netscape Navigator or "pull" the image off of your broswer window and then reopen the image in Photoshop. To achieve best quality you should save these jpeg format images and open them in NIH Image for Macintosh, Scion Image for PC or Macintosh, Image/J (a free image analysis Java applet based on NIH Image), or Photoshop. For details on processing, imaging, and calibration, please read our Procedures page. If you are interested in setting up your own online slide database with FileMaker, look at our MBL setup tutorial.

The MBL is a collaborative project between Robert W. Williams (Center for Genomics and Bioinformatics, University of Tennessee) and Glenn D. Rosen (Department of Neurology, Beth Israel Deaconess Medical Center, Boston). Programming and interface are by Alexander G. Williams. The MBL currently runs on a set of Macintosh G4 computers at the University of Tennessee.

Please use an up-to-date browser (version 4.5 or higher), and assign your program 12 MB or more of memory. If images appear heavily pixelated or lack grayscale tone, then your browser is probably low on memory.

Example Slide

Example of a 1-in-10 series of Nissl-stained horizontal sections (30-µm-thick) prepared from a C57BL/6J male mouse (Case 232, slide A, 476-mg brain weight, 292-days-old). The highest or most dorsal section is in the upper left corner; the lowest or most ventral section is in the lower right quadrant. Small dots over the tissue represent sample sites used for high-magnification cell counts and to estimate brain volume after processing. To minimize sample periodicity and to ensure a more represetative set of sample sites, the 2-mm grid has been oriented at an angle of 5 degrees. Four such slides are prepared for every case, and images of two of these four slides are now available on-line for image and data analysis. This particular brain contains 75 million neurons, 23 million glial cells, 7 million endothelial cells, and 3 to 4 million miscellaneous pial, ependymal, and choroid plexus cells (see data analysis in Williams, 2000). This section is currently mounted on the iScope and you can image individual cells in any of the sections.

Use of Images and Citing this Source

Use of images: All individuals and organizations (for-profit and not-for-profit) may use up to 10 images from the Mouse Brain Library in single works or publications and presentation. Please see the paragraph below for citing the MBL. If you or your colleagues need original uncompressed images in color we should be able to recapture and send you what you need in less than 48 hours. We would greatly appreciate an email telling us what images you are using and how you are using them. This informations will of significant help to us in securing continued support for the MBL. Please contact us ( and for more extensive or commerical use of images.

How to cite the MBL in papers: Please cite either or both of these references:

Rosen GD, Williams AG, Capra JA, Connolly MT, Cruz B, Lu L, Airey DC, Kulkarni K, Williams RW (2000) The Mouse Brain Library @ Int Mouse Genome Conference 14: 166.

Williams RW (2000) Mapping genes that modulate mouse brain development: a quantitative genetic approach. In: Mouse Brain Development (Goffinet AF, Rakic P, eds). Springer, New York, pp 21–49.


Rob and Glenn thank the following co-workers for helping us assemble the MBL since its inception in 1996: David C. Airey, Tony Capra, Michael T. Connolly, Brian Cruz, Richard Cushing, Jason Dapper, Dan Goldowitz, Diane B. Hall, Aaron Levine, Lu Lu, Anna Ohlis, Stefany Palmieri, Johnathan Wang, Alexander G. Williams, Evan G. Williams, Guomin Zhou, Xiaoyu Zhou, Boris Diechtiareff, Thomas Fackler, Nathan La Porte, Arthur G. Centeno, Senhua Yu, Chris Vincent, Leslie Lyness, and Tisha Milburn.

The MBL and iScope projects are supported as part of the Informatics Center for Mouse Neurogenetics, a Human Brain Project/Neuroinformatics program funded jointly by the National Institute of Mental Health, National Institute on Drug Abuse, and the National Science Foundation (P20-MH 62009).

Last update: October 25, 2011. MBL web service initiated Dec 8, 1996.

A Human Brain Project/Neuroinformatics program funded by the National Institute of Mental Health,
National Institute on Drug Abuse, and the National Science Foundation (P20-MH 62009).
Web server statistics report since October 11, 2004 is available here

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