Whole Brain Microscopy Facility 

The Whole Brain Microscopy Facility (WBMF), part of UT Southwestern's Department of Neurology and Neurotherapeutics, was established in 2014 and is supported by the Texas Institute for Brain Injury and Repair.

The facility is particularly well-suited to advance the study of traumatic brain injury, as well as other neurological and psychiatric disorders. We utilize cutting-edge microscopy strategies to evaluate neuropathology across micro-, meso-, and macro-scales of inquiry. These techniques enable the tracing of neuronal projections from injured sites to their long-range targets, allowing crucial and previously unfeasible studies into the altered connections established by neurons following brain injury.

Denise Ramirez, Ph.D., Core Manager, and Julian Meeks, Ph.D., WBMF Director, with the Tissue Vision TissueCyte 1000.
Denise Ramirez, Ph.D., Core Manager, and Julian Meeks, Ph.D., WBMF Director, with the TissueVision TissueCyte 1000.

We provide access to several high-throughput microscopes for UT Southwestern and external researchers:

TissueVision TissueCyte 1000

The facility houses two state-of-the-art TissueCyte 1000 multi-photon microscopes with integrated precision vibratomes for automated sectioning and imaging of the entire volume of a mouse brain in approximately 10 hours. Typical resolutions are approximately 1 micron in the x-y dimensions and 50 to 100 microns in the z dimension, but with a combination of optical and physical sectioning, a z-resolution of 1 micron can be obtained. Brains from mice with a variety of fluorescent reporters can be imaged (e.g. transgenic animals expressing fluorescent proteins such as GFP, tdTomato or mice injected with fluorescent tracers). Perfusion-fixed mouse brains are delivered to the facility for imaging by our personnel.

Hamamatsu NanoZoomer 2.0-HT

The NanoZoomer 2.0-HT is a digital slide scanner that converts glass slides into high-resolution digital data by high-speed scanning (approximately 60 sec for a 15x15 mm brightfield sample at 20X). This user-friendly scanner is designed to process up to 210 slides automatically with outstanding image quality in both brightfield and fluorescence modes. The Z-stack function of the NanoZoomer 2.0-HT allows whole slide multilayer scanning with the ability to navigate through multiple focus planes. The fluorescence module enables imaging of GFP or Texas Red fluorescent signals. After training, users can schedule time to scan their own slides or WBMF staff can scan your slides for you.

Zeiss Axioscan.Z1

The Zeiss Axioscan.Z1 is a digital slide scanner that converts glass slides into high-resolution digital data by high-speed scanning in both brightfield and fluorescence modes. Up to 100 slides can be scanned automatically. The machine features sensitive cameras, highly corrected optics and perfected light sources for exceptional image quality in your virtual slides and short exposure times to reduce photobleaching. Both standard (26 mm x 76 mm) and large-format (52 mm x 76 mm) slides can be scanned at 20X or 40X resolution. DAPI, GFP, Cy3/Texas Red, and Cy5 fluorescent signals can be imaged in the same samples. The images can be viewed in the free ZenLite software. After training, users can schedule time to scan their own slides or WBMF staff can scan your slides for you.

Other Equipment

The WBMF also offers access to a fluorescence stereomicroscope and upright microscope, both with digital cameras, as well as sectioning equipment (cryostat, microtome, and vibrotome). Additionally, we have a powerful workstation computer available for use running MicroBrightField’s Stereo Investigator and Neurolucida software packages for offline stereological analysis, neuron tracing, and 3D rendering of large, whole-brain datasets.

Serial two photon images encompassing the entire volume of the mouse brain were collected on the TissueCyte 1000 and rendered in three dimensions. Brain contains both GFP and tdTomato. (Sample credit: Drs. Asghar Talebian and Mark Henkemeyer, UT Southwestern Department of Neuroscience).

Other Services

Frozen sectioning (cryostat or microtome), general histological staining such as H&E, cresyl violet, or Luxol Fast Blue, and immunostaining.

iLab

All of our equipment scheduling and service requests are handled online through our lab management software platform, iLab. Contact Denise Ramirez for more information on setting up your iLab account.

BioHPC

The Whole Brain Microscopy Facility is pleased to offer our users 250GB of free cloud based image storage through our association with the UT Southwestern BioHPC. Please contact Denise Ramirez for further information on setting up your cloud storage account.