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Spatial Profiling Platform & Microscopes

Coming soon: 10x Genomics Atera

Whole slide, whole transcriptome imaging on any regular slide! 

10x Genomics Xenium Analyzer

​Xenium analyzer is a highly-multiplexed and sensitive imaging platform for RNA targets. It allows profiling transcriptome at single-cell and sub-cellular resolution.
Objectives:

  • 20x water

Sample type: FFPE or Fresh Frozen of both mouse and human
Available Panels: 10x Genomics Panels with customized add-on options
Operating software: Xenium Ranger, Xenium Analyzer
Location: Longwood Center Basement Rm 1055C
Contact person: Dr. Kun Huang

 

Current Xenium Panels (FFPE & Fresh Frozen)

Human:

  • 5K Pan Tissue & Pathways Panel 5000+100 customize
  • Immuno-Oncology 380+100
  • Multi-Tissue and Cancer 377+100
  • Breast 280+100
  • Brain 266+100
  • Lung 289+100
  • Skin 282+100
  • Colon 322+100

Mouse:

  • 5K Mouse Pan Tissue & Pathways Panel 5000+100
  • Brain 247+100
  • Tissue Atlassing 379+100

 

Akoya PhenoCycler (CODEX) coupled with ZEISS Axio Observer 7

CODEX is a fast, unbiased, and highly-multiplexed imager for protein targets. It allows the phenotyping of millions of cells in complex tissue or environment as a single intact tissue section. 

Pushing the frontiers of spatial biology, our team offers services from tissue staining, to imaging, to machine-learning based cell segmentation and analysis.
 

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Instrument:

  • PhenoCycler (formerly CODEX) perfusion system
  • ZEISS Axio Observer with Colibri 7 LED light Source

Objectives:

  • 10x air
  • 20x air

Excitation wavelength:
385 nm, 469 nm, 555 nm, 631 nm, 750 nm

Sample type: Mouse Fresh Frozen, Human FFPE
 
Operating software: Zen Software, Akoya Software
Location: Longwood Center Basement Rm 1055C
Contact person: Dr. Kun Huang

Antibody panels are available upon requests. Please email Kun_Huang@dfci.harvard.edu


​Image Analysis HP Workstation

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​The HP workstation offers high-computing power for fast 3D reconstruction, image quantification and segmentation. 

Software installed:

  • Zen desk (full version module)
  • Fiji (ImageJ)
  • CellProfiler (with CellPose and StarDist)
  • CODEX processor
  • QuPath
     


THUNDER Imager 3D Cell Culture

THUNDER Imager is a wide-field microscope that allows high-speed and high-quality 3D exploration of whole organisms, tissues, or cells. It features "Computational Clearing," which eliminates out-of-focus blur and enables shading correction. The microscope offers an environmental enclosure (temperature, humidity, and CO2 control), as well as an auto-focus to maintain samples at the focal plane over time. In addition, the instruments' “Spiral” option offers efficient tile scan imaging.
 

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Applications:

  • Widefield imaging up to 8 channels.
  • DIC
  • Phase Contrast
  • Polarizing microscopy
  • Live-cell imaging

Objectives:

  • Leica N Plan 5x/0.12 PH 0
  • HC PL FLUOTAR 10x/0.32
  • HC PL APO 20x/0.80
  • HCX PL APO 40x/1.10 W CORR
  • HC PL APO 63x/1.40-0.60 OIL

Excitation wavelengths:

390 nm, 440 nm, 475 nm, 510 nm, 555 nm, 575 nm, 635 nm, 747 nm.

Detectors: two QUAD cubes

  • DFT5 for DAPI/FITC/TRITC/Cy5
  • CYR7 for DFP/YFP/Texas Red/Cy7

Slide holder types:

  • Universal holding frame K
  • 4-Slide insert
  • Holding frame KM for Well Plates

Operating software: Leica LAS X Software
Location: Longwood Center Basement Rm 1055D
Contact person: Paul Speliakos
 

Zeiss 980 Confocal/Spectral/Airyscan


The LSM 980 microscope is a fully automated multimodal microscope that can be used for confocal, and spectral imaging. It is equipped with a unique AI Sampler Finder System. 

The Airyscan detector enables super-resolution and high-speed imaging. The LSM 980 is also equipped with Near-IR detectors that expand imaging spectra from UV to NIR.

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Applications:

  • Confocal imaging
  • Spectral imaging with linear unmixing
  • Super-resolution imaging with resolution up to 90 nm using Airyscan
  • Forster Resonance Energy Transfer (FRET)
  • Fluorescence Recovery After Photobleaching (FRAP)
  • Tile scan

Objectives:

  • 5x air
  • 10x air
  • 20x air
  • 25x multi-immersion (water, silicone oil, glycerin, oil) objective with 0.57 mm working distance
  • 63x 1.4 oil
  • Alpha Plan-APO 100x/1.46 Oil DIC VIS

Laser lines:
405 nm, 445 nm, 514nm, 561 nm, 594 nm, 639 nm, 730 nm

Detectors:

  • 34 Channel Quasar Detector Array
  • Airyscan 2 Detectors
  • Near-IR detectors (Filter set 8 deep red 640 +730 nm f/NIR and filer set 9 deep read 730 f/NIR)

Slide holder types:

  • Scanning Stage (with Z-piezo)

Operating software: Zen Software
Location: Longwood Center Basement Rm 1055E
Contact person: Dr. Kun Huang