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SEM View

SEM View shows a segmented image the way a scanning electron micrograph of a cut surface would: you see into the pores, and surfaces farther below the cut look darker. Use it to read depth into a stack of black-and-white slices, or to compare an image with a micrograph of the same material. It's a rendering, not a simulation of the instrument.

  • Find it Tools › Visualize › SEM View
  • Needs a segmented 3D image, up to 1024³ voxels
  • Returns three depth-shaded views, one for slicing normal to each axis, stored with the image and shown in a slice viewer
  • Runs on CPU
  • Science SEM View

Run it

  1. Open Tools, then Visualize, and select SEM View. You can also start from an image's page, which fills in the image for you.
  2. Under Source, choose the Image, or a batch to run every image in it.
  3. Leave Force regenerate fields unticked unless you want to rebuild views the image already has.
  4. Select Run. The job page opens and follows the job until it finishes.

The SEM View launch form with an image chosen.

Choose the image; tick Force regenerate fields only to rebuild existing views.

Settings

Setting Default Range What it does
Image your team's images and batches The image to render, or a batch to run one job per image.
Force regenerate fields off on, off Rebuilds the views even if the image already has them.

The views are stored with the image, not the job. When an earlier SEM View run on the image completed and its views are still there, a new run reuses them unless you tick Force regenerate fields. Saving an edit over the image removes them, and the next run rebuilds them.

Results

The job page shows the SEM View in a viewer of three orthogonal panels, XY, XZ and YZ, each shaded for slicing normal to its own axis. Click a panel to move the crosshairs; the other two panels follow, and the read-out gives the X, Y and Z of the point. Solid cut by the plane is brightest, and pores fade to dark with depth.

A small example on a 120³ synthetic sample. Left: its middle slice. Middle: the SEM View of the same plane, where solid farther behind the plane looks darker. Right: the X-Ray View along the same axis.

A completed SEM View job with three depth-shaded orthogonal panels.

Click a panel to move the crosshairs; the position shows at the top right.

Common problems

  • The run finished at once and nothing looks new. The image already had its views, and the run reused them. Tick Force regenerate fields to rebuild them.
  • Pores at one edge look shallow. Depth counts from the image's edge, so a pore open to the edge at index 0 looks shallower than it is.
  • Comparing two images. Brightness is relative to each image's deepest pore, so compare grey levels within one image, not between images.
  • The image is too large. SEM View takes up to 1024³ voxels. Trim the image first.

Science

How depth is counted and turned into brightness: SEM View in the Scientific reference.