Knife Edge Scanning Microscope

3Scan images entire sample volumes of over 100 cm3 at cellular level resolution, combining elements of non-invasive radiology and light microscopy. Our KESM can process up to 3,600 slices per hour (e.g. a whole mouse brain) of any tissue sample at submicron resolution (a voxel size of 0.6 um x 0.7 um x 1.0 um).

To handle data outputs of up to a terabyte per cm3, 3Scan has built customized processing and analysis software. 3Scan offers data processing software to model 3D tissue reconstructions, provide interactive image views, and apply quantitative analytics

The unprecedented volume of high-resolution 3D data generated by the KESM opens up a new realm of possibilities for meso-and micro-scale insights.

Applications include:

  • Large volume 2D fly-throughs (~200-800 sections per cm3)
  • 3D visualizations and models of various tissues (i.e. tumor morphology)
  • Co-registration of features from non-invasive radiology and light microscopy
  • Automated quantification and analysis of specific tissue structures (e.g. microvasculature)

The KESM is a Knife-Edge Scanning Microscope that produces digital 3D tissue models at micron-scale resolution. Using a diamond bladed knife, nano-positioned motions, and proprietary optics, the KESM deliver trillions of voxels per day at 400 times the throughput of traditional microscopes.

The KESM moves in strips across the surface of a block of tissue, slicing and scanning simultaneously. As the tissue is coming off the knife, it captures one line at a time of image data, ensuring precise spatial alignment. Once the KESM has sliced a layer off the entire surface, it moves down a few microns, slices the next surface, and then repeats this process until it has consumed the entire tissue volume.

New levels of discovery

Whole Murine Kidney, turntable

(india-ink-stained, resin-embedded)


Murine Kidney Glomeruli

(india-ink-stained, resin-embedded)


Murine Kidney Vasculature, 2D Fly-Through:

(india-ink-stained, resin-embedded)

Open Data

3Scan believes strongly in Open Science and Open Data. If you have questions about this data are would like to use it in your research please don’t hesitate to contact us at info [at] or on twitter at @3scantweets

Vascular Fingerprint Open Data Sets

Tile Server Data

Open Training Data

Other Available Data Sets from 3Scan:

Whole mouse kidney (india-ink-stained, resin embedded)

Whole mouse colon (H&E-stained, paraffin embedded)

All links listed below here can be used directly as html resources

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