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napari-isbem

napari-isbem is a napari plugin to enable targeted acquisition of samples in Serial Block-Face Scanning Electron Microscopy (SBF-SEM). Coordinates of regions of interest can be found using non-destructive X-Ray Microscopy (XRM) images. The plugin interfaces with the open-source acquisition software SBEMimage to update acquired sections in real-time during imaging.

The main workflow is described below:

  1. In the Targeting tab, import the OME Zarr targeting image and create or import desired ROIs.
  2. To view the SBF-SEM data, select the overview directory of the current SBEMimage project in the Acquisition tab. The napari viewer is automaically updated when new images are acquired.
  3. Align the targeting and SBF-SEM images in the Registration tab to obtain ROI coordinates relative to the SBF-SEM data.
  4. Start the TCP server in the Acquisition tab and select the registered ROI layer. Continue the SBEMimage acquisition with Use TCP enabled to automatically image ROIs.