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VUMC DHSR (Digital Histology Shared Resource)

Overview of Services

 

The Digital Histology Shared Resource provides large-scale digital archiving and quantitative analysis of histologic, immunohistochemical and immunofluorescence staining of tissue sections and tissue microarrays and houses an array of sofisticated whole slide imaging platforms:

  • Aperio Versa 200 (Leica/Aperio) Automated Slide Imaging System for bright field and fluorescence whole-slide imaging. This platform holds up to 200 slides per batch; has 6 separate filter channels: DAPI, Cy2, Cy3, TxRed, Cy5, and Cy7. It is the ideal system for rapid, automated, and consistent whole-slide imaging in a wide range of fluorescent channels and bright field modalities. The DHSR operates two identical Aperio VERSA 200 systems, alowing for double the throughput.

  • Aperio AT2 400 (Leica/Aperio) This whole-slide imaging system from Leica can hold up to 400 slides per batch and has greatly improved speed and image quality. This is the standard imager for clinical samples.
  • SCN400 (Leica) Automated Slide Scanner for bright field whole-slide imaging: this platform is ideal for large cohorts of samples. It is capable of processing up to 384 slides per batch. All imaging settings (white point, Köhler illumination, etc.) are computer-controlled for highly consistent results batch to batch. This system has been the workhorse for the DHSR for a number of years.

  • Cell DIVETM platforms (Leica/Cytiva - formerly GE Healthcare): The DHSR houses both the prototype CellDiveTM system consisting of a modified GE Cytell scanner with upgraded camera, lamp, and objectives, as well as the first commercial release version utizling the new InCell 2500 scanner. Both imaging systems have 4 filter channels: DAPI, Cy2, Cy3, and Cy5. They are paired with an HP Z840 workstation which runs the LayersTM MxIF image analysis software (GE) needed to segment and analyze the large data sets produced by the CellDiveTM.

  • Digital Slide Archive (Emory/Kitware) web-based digital whole slide review and analysis platform: an extremely versatile online viewer for whole-slide images. This easy to use digital slide box allows DHSR users to view, annotate, analyze, and share all of the slides no matter where they, or their collaborators, are. This system also allows researchers to download origial copies of their whole slide images.

  • eSlideManager (Leica/Aperio) web-based digital whole slide review, sharing, annotation, and analysis platform. This software is the modern upgrade to the aging Digital Image Hub with tighter cybersecurity, better searching and desktop features. This software is capable of auto uploading images directly from the Aperio AT2 400 into its database.

  • Analysis and computational power: The DHSR hosts ~50TB of whole slide images on 120TB of the VUMC petabyte array, as well as over 150TB of local RAID6 storage to gaurd against data loss. Additionally, five HP workstations (Z8-series) with large formatscreens (>=43”)  are utilized by the DHSR for image quantification and export. The automated imaging and analysis performed in this core saves researchers and staff weeks of tedious work. An additional service offered by the DHSR is the creation of digital archives of critical and irreplaceable tissue samples, a benefit only feasible due to the automated high-resolution imaging of whole 25 mm x 75 mm microscope slides and 50 mm x 75 mm slides.

  • GelCount system by Oxford Optronix scans and counts mammalian organoids and yeast or bacterial colonies in a wide variety of Petri dish and cell culture plate formats. This system is designed for the detection, counting and characterization of stained/adherent mammalian cell colonies or of unstained/non-adherent colonies in soft agar or collagen assays, but also works very well for yeast and bacterial colonies. The software is fully trainable and can be programmed to recognize specific colony features. Detailed information such as diameter, area, density, and nearest neighbor is provided, as well as high-resolution images.

 

          

 

 

To Submit Slide Submission Requests:  Click the Request Services Tab

To Reserve an Instrument:  Click the Schedule Equipment Tab

 Links and Resources

DHSR Website: https://www.vumc.org/dhsr/
Digital Slide Archive:  https://digislide.app.vumc.org
eSlideManager: https://eslidemanager.app.vumc.org

 

 Leadership

Scientific Director:  James R. Goldenring, M.D., Ph.D.

Managing Director:  Joseph T. Roland, Ph.D.

For additional information, please contact us by email at Digital.Histology@vumc.org

 

Location and hours of operation

Hours Location

Monday-Friday
9:00 a.m. - 6:00 p.m.                 

10425 MRB IV      

Acknowledge the DHSR in publications:
Please remember to acknowledge the DHSR in your publications, in talks, and on posters. Use the text below that is appropriate:

For whole slide imaging and quantification:
Whole slide imaging and quantification of immunostaining were performed in the Digital Histology Shared Resource at Vanderbilt University Medical Center (www.mc.vanderbilt.edu/dhsr).

For whole slide imaging:
Whole slide imaging was performed in the Digital Histology Shared Resource at Vanderbilt University Medical Center (www.mc.vanderbilt.edu/dhsr).

For colony counting:
Colony imaging and quantification was performed on the GelCount System (Oxford Optronix) in the Digital Histology Shared Resource at Vanderbilt University Medical Center (www.mc.vanderbilt.edu/dhsr).

 

Billing Number Activation

 VUMC Investigators with VUMC center numbers:
  All VUMC billing numbers are activated in iLab via a nightly feed from Workday. Grant Worktags are auto-assigned to the PI's lab group. All other funds (Cost Centers, Gift or Program Worktags) must be claimed within the PI's Lab Group.
 
 VU Investigators with VU CoA or POET numbers:
  VU users will manage the VU billing numbers via the webform on the VUMC Office of Research website
 
 Vanderbilt Investigators with VA (Veteran Affairs) funding: 
  Contact the VUMC Office of Research at VUMCcores@vumc.org to request access to your VA funding.  All investigators with VA funding are assigned a VA billing number (999999xxxx). The VUMC Office of Research manages VA billing numbers in coordination with the VA Research Administration.
 
 

 

 


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