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- STEREOLOGY IHC AXIO SERIAL
- STEREOLOGY IHC AXIO REGISTRATION
- STEREOLOGY IHC AXIO SOFTWARE
- STEREOLOGY IHC AXIO FREE
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. If you have an existing iLab account set up for another core, it can be utilized to gain access to our core services as well. Contact Denise Ramirez for more information on setting up your iLab account as an internal or external user of the facility.
STEREOLOGY IHC AXIO SOFTWARE
iLabĪll of our equipment scheduling and service requests are handled online through our lab management software platform, iLab. We stock a panel of commonly used neuroscience antibodies directed against NeuN, GFAP, Iba1, CD31, MBP, and TuJ1/Beta III tubulin, or we can optimize a staining protocol and detection method for your experiment. General histological staining such as H&E, Nissl/cresyl violet, or Luxol Fast Blue.
STEREOLOGY IHC AXIO SERIAL
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The Z-stack function of the NanoZoomer 2.0-HT allows whole slide multilayer scanning with the ability to navigate through multiple focus planes. This user-friendly scanner is designed to process up to 210 slides automatically with outstanding image quality in both brightfield and fluorescence modes. 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). Automated analysis services are performed by our full-time computational scientist. The fully automated nature of the TissueCyte serial two photon system coupled with the robust analysis pipeline is amenable to processing large numbers of experimental animal brains (mouse and rat).
STEREOLOGY IHC AXIO REGISTRATION
The pipeline includes pixel classification using supervised machine learning, registration of fluorescent signals into the field standard average mouse brain atlas (Allen Institute for Brain Science Common Coordinate Framework, v3.0) and automated quantification of fluorescent signals of interest across every brain region (see Ramirez et al., Multiphoton Microscopy 2019). We also offer a fully developed, automated image analysis pipeline for use on whole brain volumetric images collected on the TissueCyte.
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Perfusion-fixed mouse brains are delivered to the facility for imaging by our personnel. transgenic animals expressing fluorescent proteins such as GFP, tdTomato or mice injected with fluorescent tracers). Brains from mice with a variety of fluorescent reporters can be imaged (e.g. 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. 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. The WBMF provides access to a unique set of high-throughput microscopes and histology resources for UT Southwestern and external researchers, ideally suited for cutting-edge neuroscience research. 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 utilize cutting-edge microscopy strategies to evaluate neuropathology across micro-, meso-, and macro-scales of inquiry. The facility is particularly well-suited to advance the study of traumatic brain injury, as well as other neurological and psychiatric disorders.
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and is supported by the Texas Institute for Brain Injury and Repair The facility was established in 2014 under the leadership of Dr. and is part of UT Southwestern's Department of Neurology and the Peter O'Donnell, Jr. The Whole Brain Microscopy Facility (WBMF) is directed by Dr.