Slide scanning at the
AMI Imaging Centre

TissueGnostics TissueFAXS SL

Automated slide scanning microscopes can provide numerous benefits in various areas of biomedical research such as pathology, histology, neuroscience, drug discovery, and developmental biology. The AMI slide scanner can image slides efficiently in high resolution using an automated slide loader, thus improving the throughput and impact of experiments and allowing researchers to generate large amounts of data to yield insightful results. This is achieved by taking a series of high resolution images across the entirety of the sample and accurately combining the images to produce a single, highly detailed image of the full slide sample.

By using transmitted light microscopy (i.e., for hematoxylin and eosin stains), or fluorescence microscopy (i.e., for immunofluorescence labelling), the AMI automated slide scanner can provide detailed spatial information at comprehensive scales when imaging fixed samples prepared on slides. Small organs, for example, can be sectioned and imaged in their entirety to provide a complete and contextualised map of biological information. For other applications, the slide scanner can be used to efficiently capture morphological data of hundreds of patient-derived biopsy samples. When combined with powerful machine learning analysis pipelines, the slide scanner can help decipher highly complex and detailed biological observations at unprecedented scales and numbers.

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Tissue cytometry

When using high-resolution objective lenses and tissue cytometric workflows, the AMI slide scanner enables visiting researchers to measure and analyse fixed tissues or cell culture monolayers—providing both biochemical information (in the form of signal intensity) as well as spatial information (in the form of relative signal location) at the cellular level. Therefore, powerful information can be gained into cellular interactions, distributions, population structures, and spatial correlations. This can be used to identify new sample characterisations that best describe the biology being investigated.

Instrument specifications

• Upright microscope configuration

• Contrast methods:

  • bright-field transmission

  • fluorescence (Lumencor SPECTRA Light Engine)

• Automated loading of standard and over-sized slides

  • Max. 120 slides​

  • Sample ID/label scanner

• Automated acquisition

  • Sample detection algorithm

  • On-the-fly focus assessment and re-acquisition

• Acquisition objectives:

  • 40× 0.95 NA with correction collar (370×370µm FOV)

  • 20× 0.8 NA (750×750µm FOV)

  • 10× 0.45 NA (1.5×1.5mm FOV)

• Transmitted light source

• Compatible channels:​

• • DAPI (Em: 375-407nm)

  • FITC (Em: 463-496nm)

  • TRITC (Em: 542-566nm)

  • CY5 (Em: 622-653nm)

  • CFP (Em: 422-450nm)

  • YFP (Em: 495-516nm)

  • Texas Red (Em: 566-590nm)

  • Cy7 (Em: 710-750nm)

• Monochrome sCMOS camera

  • Hamamatsu Orca Fusion BT C154440​

• Colour CMOS camera​

Instrument capabilities

• Resolution: down to ~500nm

• Speed: 120 slides in 8-36 hours (magnification dependent)

• Sample thickness: max. ~50µm

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Instrument uses

• Extended focus imaging

• Z-Stack 3-D imaging

• Large-scale screening

• Sample characterisation and tissue analysis

• Histopathology quantification

• Immunohistochemistry

• Fluorescence in vitro hybridization (FISH)

• Spatial transcriptomics

• Quantification of stained tissues (i.e., Giemsa, Periodic acid–Schiff, hematoxylin and eosin) 

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