Whole Brain Microscopy Services & Fees
3D Volumetric Imaging and Automated Analysis
We can generate high-resolution, whole-brain/whole-tissue 3D images as a full-service operation using serial two-photon tomography (STPT) or lightsheet microscopy according to specific experimental needs. Fixed specimens can be provided to the core, and we can take it from there. Core staff can perform STPT or tissue clearing using the Clear+ method, whole-brain/whole-tissue immunostaining, and lightsheet microscopy on your fixed specimens. If you prefer to use the lightsheet microscope independently, training can be arranged. Following whole-brain image acquisition, our computational team can use our custom-developed registration and analysis pipelines to align your whole-brain image into a reference atlas and quantify the brain-wide distribution of your fluorescent signal of interest.
Fees
- Lightsheet microscopy
Category Fee (UTSW user) Unit Training $144 one time SmartSPIM self-use after training $26 hourly Full-service lightsheet imaging by WBMF staff $52 hourly Use of SmartBatch for active electrophoresis (immunostaining) $103 daily - Serial Two-Photon Tomography (STPT) & Image Analysis
Category Fee (UTSW user) Unit Mouse brain, 0.875 x 0.875 x 25um resolution $515 per brain Rat brain, 0.875 x 0.875 x 100um resolution $721 per brain Mouse brain, standard resolution, with section capture $721 per brain Mouse cervical spinal cord segment, 0.875 x 0.875 x 20um resolution $200 per cord segment Image Analysis
The WBMF staff conducts full-service image analysis.
Category Fee (UTSW user) Unit Pixel classification services by WBMF staff in ilastik $52 per brain Probability map output (classified images) $26 per brain Whole mouse brain registration and quantification $52 per brain
Histology Services
We offer full frozen sectioning using cryostat or microtome, for brain or other tissues. We offer general histological staining such as H&E, Nissl/cresyl violet, or Luxol Fast Blue, or immunostaining. 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.
Fees
- Tissue Sectioning | Histology
Category Fee (UTSW user) Unit Training - cryostat $31 one time Training - microtome or vibrotome $16 one time Cryostat self-use after training $12 hourly Microtome self-use after training $7 hourly Vibrotome self-use after training $7 hourly Full-service cryosectioning by WBMF staff, plus slide and box costs $52 hourly Full-service histological staining by WBMF staff $52 hourly Full-service immunostaining by WBMF staff $52 hourly
Whole slide scanning
We can conveniently scan your slides for you in brightfield or fluorescence mode and return the images to you via Box link. No training or setup time needed on your side!
Fees
- Slide Scanning
Category Fee (UTSW user) Unit Slide scanner training $72 one time Nanozoomer self-use after training $23 hourly Axioscan self-use after training $23 hourly Full-service slide scanning by WBMF staff $45 hourly
Miscellaneous
- Image Analysis
Category Fee (UTSW user) Unit Training to use ilastik or QuPath $72 one time GPU workstation (Imaris) self-use $21 hourly Microbrightfield Bioscience workstation (Neurolucida 360, Stereoinvestigator) self-use $16 hourly - Small Microscopes
Category Fee (UTSW user) Unit Training - Upright or Stereo Epifluorescent microscopes $16 one time Zeiss Axioscope.A1 upright microscope for self-use after training $7 hourly Leica MZ10F stereomicroscope self-use after training $7 hourly
BioHPC
The Whole Brain Microscopy Facility is fully integrated with the state-of-the-art cluster computing resources available through UT Southwestern’s BioHPC. The use of BioHPC to transfer and store large datasets generated in the facility is a suitable option; however, the UTSW implementation of Box, now available to all employees, may be preferred. All UT Southwestern O’Donnell Brain Institute (OBI) Investigators can gain access to BioHPC resources. Please contact Denise Ramirez for further information on setting up your BioHPC account.