The Whole Brain Microscopy Facility (WBMF) uses cutting-edge microscopy strategies to advance the study of traumatic brain injury as well as other neurological and psychiatric disorders. We are also available to investigators working in other organ systems.
We offer a variety of unique microscopes capable of automatically acquiring high resolution volumetric images.
The facility houses two state of the art TissueCyte 1000 multi-photon microscopes with integrated precision vibratomes to generate high resolution images of whole, uncleared brains or other organs using serial two-photon tomography (STPT). The facility employs a full time computational scientist who is engaged in the development and implementation of sophisticated computational strategies for the analysis of volumetric data.
We have two digital slide scanners, the Zeiss Axioscan and Hamamatsu Nanozoomer, which allow for the creation of whole slide images (WSI) in both brightfield and multichannel fluorescent modes.
We also offer a variety of standard histological services such as frozen sectioning, histological staining, and immunostaining which are performed by our full time histology technician.
Frozen sectioning services are limited to local (Dallas-Ft. Worth area) clients but we accept clients from any location worldwide for our other services.
The facility houses two state-of-the-art TissueCyte 1000 multi-photon microscopes (TissueVision, Inc.) with integrated precision vibratomes for automated sectioning and imaging of the entire volume of a mouse brain (or other organs) in approximately 10 hours at the standard resolution. 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 3 micron can be obtained. Brains from mice or rats 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). The brains do NOT require clearing for this imaging method, but DO require the presence of an inherent fluorescent signal. Perfusion-fixed mouse brains are delivered to the facility for imaging by our personnel.
Please see the "Lab photos" section for some representative whole brain images.
Resultant 2D and basic 3D images will be provided to the client using our cloud server. Quantitative analysis of whole brain datasets can be performed for an additional fee (dependent on data quality and desired parameters) - please specify if you are interested in this service in your request.
Pricing is dependent on desired resolution and number of samples.
Automated image analysis for whole brain serial two-photon images acquired using TissueCyte serial two-photon system. Our pipeline includes machine learning based signal segmentation and registration of the resultant probability map output into the standard mouse brain atlas created by the Allen Institute for Brain Science, the Common Coordinate Framework, v3.0. Fluorescent signals of interest can then be quantified in every annotated brain region and displayed visually within the atlas volume (see Lab Photos). This facilitates analysis and comparison of signals in large cohorts of experimental animals. Pricing is project-dependent.
Whole fixed brains from mice or other species can be automatically sectioned and imaged throughout the entire volume using the TissueCyte serial two photon microscope (see Serial Two-Photon Tomography service listing).
Volumetric images acquired on the TissueCyte 1000 serial two-photon tomography system can be registered into the standard mouse brain atlas generated by the Allen Institute for Brain Science, the Common Coordinate Framework v3.0. (see Automated Image analysis service listing).
We have two whole slide scanners in the facility: the Zeiss Axioscan.Z1 and the Hamamatsu Nanozoomer 2.0-HT.
The Zeiss Axioscan.Z1 is optimized for multichannel fluorescence scanning, but can scan in brightfield mode as well. 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.
The NanoZoomer 2.0-HT is preferred for high-speed brightfield scanning with exceptional image quality (approximately 60 sec for a 15x15 mm sample at 20X). This user-friendly scanner is designed to process up to 210 slides automatically, combining high throughput 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 subsequent advantage to navigate through multiple focus planes. The fluorescence module enables imaging of GFP or Texas Red fluorescent signals. The images can be viewed in the free, user-friendly NDPview2 software as well as the free Leica Aperio Imagescope program.
We can provide access to whole slide image files through our cloud server upon completion.
Slide scanning is billed hourly, not per slide.
We can prepare cryosections on your fixed tissue samples from mouse, rat, human or other species. We have extensive experience in frozen sectioning methods utilizing both cryostat and microtome sectioning. We can perform cryoprotection and cryoembedding of your fixed specimens prior to sectioning as required.
We can perform histological staining and/or immunostaining of your prepared frozen sections on site for an additional fee.
Pricing is project-dependent.
We can perform immunostaining detected with colorimetric (DAB) or fluorescent methods, using your primary antibody or one of our stock primary antibodies. We can return immunostained slides to you for imaging or we can image them on site using whole slide imaging or other methods as appropriate. We stock these primary antibodies:
anti-NeuN (neuronal marker)
anti-GFAP (astrocyte marker)
anti-MBP (myelin marker)
anti-Beta III Tubulin (also known as TuJ1; neurofilament/axonal marker)
anti-PGP9.5 (peripheral nerve marker)
We stock a large variety of secondary antibodies derived from different species and conjugated to different fluorophores (Alexa dyes) or to HRP for colorimetric detection.
Pricing is project-dependent.
We can perform standard histological staining on sections you provide (paraffin or frozen) or sections prepared by our facility (frozen only). We stock reagents to perform these stains:
Hematoxylin and Eosin (H&E)
Nissl (cresyl violet)
Luxol Fast Blue
We have an upright fluorescence microscope (Zeiss Axioscope.A1) for capturing multichannel fluorescent images (DAPI, GFP, and Texas red filtersets available) or brightfield images from slide-mounted samples.
2X objective for capturing very large fields of view, plus 10X, 20X, 40X, 63X objectives are available.
We can also image your large, unmounted, fluorescently labeled tissue specimens using our Leica MZ10F fluorescence stereomicroscope. GFP and Texas red filtersets are available.
Digital image files can be provided to the client using our cloud server.
Pricing is project dependent.
Whole slide imaging using Zeiss Axioscan.Z1 and Hamamatsu Nanozoomer
"Denise and her team are amazing. They are so helpful and go beyond just providing awesome images. We will continue to work with her and give her our highest regards."
Whole Brain Microscopy Facility has not received any endorsements.