UTSW Whole Brain Microscopy Facility (WBMF)

Overview of Services

Serial two-photon images of a mouse model expressing YFP in subsets of neurons throughout the brain rendered in three dimensions. The brain was perfusion-fixed by standard methods and embedded in oxidized agarose in preparation for sectioning. The TissueCyte 1000 instrument (TissueVision, Inc.) automatically sectioned the entire volume of the brain at 100µm in the coronal plane and collected a mosaic of image tiles encompassing each section. The resulting images were corrected for uneven illumination and subjected to median filtering to reduce noise using custom MATLAB scripts. FIJI was used to stitch the processed tiles in the X-Y dimensions to create mosaic images of each tissue section. Neurolucida (Microbrightfield Bioscience) was used to render the images in three dimensions. A representative single coronal section (left panel) as well as the three-dimensional rendering of the whole brain (right panel) are shown.

The Whole Brain Microscopy Facility (WBMF), UT Southwestern Department of Neurology, was established in 2014 and is an Institutionally Supported Core (ISC). The facility is particularly well-suited to advance the study of traumatic brain injury as well as other neurological and psychiatric disorders by utilizing 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.

We provide access to several high-throughput microscopes for UT Southwestern and external researchers. WBMF houses two TissueVision TissueCyte 1000 instruments for the purpose of generating high-resolution, 3D renderings of entire rodent brains as well as four slide scanning microscopes (Hamamatsu Nanozoomer 2.0-HT, Hamamatsu Nanozoomer S60, Zeiss Axioscan.Z1 and Zeiss Axioscan 7) for the purpose of creating digital images of whole slides. We also offer cryosectioning, general histological staining such as H&E, cresyl violet, or Luxol Fast Blue, and immunostaining.

Leadership

Denise Ramirez, PhD | Director

Location and hours of operation

Hours

Location

Monday - Friday

8am - 5pm

UT Southwestern Medical Center

Dept. of Neurology

5323 Harry Hines Blvd.

Dallas, TX 75390-8813

Links and Resources

Whole Brain Microscopy Facility

Contacts

Name	Role	Phone	Email	Location
Denise Ramirez, PhD	Director	214-648-0203	denise.ramirez@utsouthwestern.edu	NL10.125B
Aleksandr Umanzor, BSc	Research Technician II		Aleksandr.Umanzor@utsouthwestern.edu	NL10.110
Li (Lily) Li, MD, MS	Histology Technician		Li.Li@utsouthwestern.edu	NL10.110
Ariana Nawaby, MS, BSc	Computational Scientist		Ariana.Nawaby@utsouthwestern.edu	NL10.108

Service list

Name	Description	Price
ilastik training	hands on training to perform pixel classification in ilastik	Inquire
Mouse brain, coronal sections, 0.875um/px lateral resolution, 10um axial resolution	3D imaging of whole brain on TissueCyte 1000 serial two-photon instrument 60um physical coronal sections collected; 8 optical planes collected per physical section at 10um apart Per brain or other similarly-sized organ of interest includes image processing to produce TIF images of whole coronal sections (~237 physical sections/brain; 1896 optical sections/brain) and basic 3D rendering to produce a lower resolution movie	Inquire
rat brain, coronal sections, 0.875um/px resolution, 100um sections	3D imaging of whole brain on TissueCyte 1000 serial two-photon instrument standard resolution, 100um coronal sections Per brain or other similarly-sized organ of interest Justification of relevance to brain injury research required to receive TIBIR support of imaging fee (50% discount). Non-CNS tissues are billed at full price. includes image processing to produce TIF images of whole coronal sections (~170 sections/brain) and basic 3D rendering to produce a lower resolution movie	Inquire

Search available services: View: by category alphabetically

Name	Description	Price
▼ ► Training (1)
ilastik training	hands on training to perform pixel classification in ilastik	Inquire
▼ ► TissueCyte Imaging (2)
Name	Description	Price
Mouse brain, coronal sections, 0.875um/px lateral resolution, 10um axial resolution	3D imaging of whole brain on TissueCyte 1000 serial two-photon instrument 60um physical coronal sections collected; 8 optical planes collected per physical section at 10um apart Per brain or other similarly-sized organ of interest includes image processing to produce TIF images of whole coronal sections (~237 physical sections/brain; 1896 optical sections/brain) and basic 3D rendering to produce a lower resolution movie	Inquire
rat brain, coronal sections, 0.875um/px resolution, 100um sections	3D imaging of whole brain on TissueCyte 1000 serial two-photon instrument standard resolution, 100um coronal sections Per brain or other similarly-sized organ of interest Justification of relevance to brain injury research required to receive TIBIR support of imaging fee (50% discount). Non-CNS tissues are billed at full price. includes image processing to produce TIF images of whole coronal sections (~170 sections/brain) and basic 3D rendering to produce a lower resolution movie	Inquire