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.

  • 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.

  • Aperio AT2 400 (Leica/Aperio): The DHSR has recently purchased a new Aperio AT2 as a replacement for the SCN400 platform. This whole-slide imaging system from Leica can hold up to 400 slides per batch and has greatly improved speed and image quality.

  • Cell DIVETM platforms (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 Image Hub (Leica) web-based digital whole slide review and analysis platform: an extremely versatile online viewer for whole-slide images. With its built-in analysis software package, 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 is currently being upgraded to the newest version from Leica (eSlideManager).

  • 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 maintains three Dell PowerEdge servers in a duplicated database to guard against data loss or corruption, hosting 42TB of whole slide images currently. Additionally, five HP workstations (Z820, Z840(2), and Z8) with large format (43”) screens are always available at 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.

  • The GelCount system by Oxford Optronix scans and counts mammalian cells, 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

 

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      

Links and Resources

  1. DHSR Website: https://www.vumc.org/dhsr/
  2. Digital Image Hub:  https://dih.emp.vumc.io

 

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).

 

 

 


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