Beth Israel Deaconess Medical Center · Harvard Medical School

Equipment

The unit operates a broad instrument base spanning imaging- and sequencing-based spatial profiling, single-cell and single-nucleus workflows, digital pathology, super-resolution microscopy, and tissue microarray construction, together with the sample-preparation and quality-control equipment that supports them.

Spatial and single-cell platforms

  • 10x Genomics Xenium - imaging-based spatial transcriptomics by fluorescence in situ hybridization, with orthogonal modalities on the same slide. See Xenium.
  • 10x Genomics Visium / CytAssist - sequencing-based spatial transcriptomics, by direct placement (fresh-frozen) and via CytAssist (FFPE and fresh-frozen, including Visium HD). See Visium / Visium HD.
  • Singular Genomics G4X - next-generation in situ spatial sequencing of RNA, protein, and morphology from a single section at subcellular resolution. See G4X.
  • Vizgen MERSCOPE - imaging-based spatial transcriptomics at subcellular resolution for targeted transcript panels. See MERSCOPE.
  • Illumina StrataMap - whole-transcriptome, sequencing-based spatial profiling at 1 µm resolution. See StrataMap.
  • Bruker GeoMx Digital Spatial Profiler - region-of-interest spatial transcriptomics and proteomics with an NGS readout. See GeoMx.
  • Akoya PhenoImager HT (Polaris/Vectra) - whole-slide multispectral imaging for multiplexed immunofluorescence with autofluorescence removal. See PhenoImager HT.
  • Akoya PhenoCycler-Fusion - highly multiplexed, iterative spatial immunofluorescence at single-cell resolution. See PhenoCycler-Fusion.
  • Bruker Vutara VXL - single-molecule-localization super-resolution microscopy for spatial studies, 3D reconstruction, and live imaging of cells, organoids, and tissue. See Vutara VXL.
  • 10x Genomics Chromium X - single-cell and single-nucleus gene expression, including from FFPE. See single-cell technologies.
  • 10x Genomics Chromium Connect - fully automated single-cell library preparation, minimizing batch-to-batch variation and maximizing throughput.

Digital pathology and tissue handling

  • Epredia / 3DHISTECH TMA GrandMaster - fully automated large-scale tissue microarrayer, combining cores from many donor blocks into recipient blocks. See TMA construction.
  • Leica BOND RX - automated immunohistochemistry and in situ hybridization.
  • Nikon Ti2 Eclipse - inverted microscope with a 25 mm field of view and large-format CMOS cameras for brightfield and fluorescence, with automated capture and large-image stitching.

Quality control and support

  • Agilent Fragment Analyzer - quality assessment of NGS libraries and RNA/DNA samples.
  • Sample preparation - Leica cryostat and microtome, laboratory refrigeration, −20 °C and −80 °C freezers, and thermocyclers.

Compute

Instrument workstations are backed by dedicated analysis servers with a local network-attached store, and the unit has access to high-performance computing for the integration and analysis of high-dimensional bulk, single-cell, and spatial data.