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Okapi-EM: A napari plugin for processing and analyzing cryogenic serial focused ion beam/scanning electron microscopy

Luís M A Perdigão1, Elaine M L Ho1, Zhiyuan C Cheng1,2

  • 1Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK.

Biological Imaging
|March 15, 2024
PubMed
Summary

Cryogenic serial plasma focused ion beam milling scanning electron microscopy (pFIB/SEM) generates 3D biological images. Okapi-EM, a new napari plugin, processes these images, improving 3D reconstruction and analysis.

Keywords:
3D imagingCryogenicimage processingnapariserial FIB/SEMsoftware

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Area of Science:

  • Electron microscopy
  • Biological imaging
  • 3D reconstruction

Background:

  • Cryogenic serial plasma focused ion beam milling scanning electron microscopy (pFIB/SEM) is an advanced technique for visualizing complex biological structures in 3D.
  • Acquired SEM images often suffer from noise, drift, and charging artifacts, hindering precise 3D reconstruction.
  • Specialized image processing is crucial for effective analysis of pFIB/SEM data.

Purpose of the Study:

  • To introduce Okapi-EM, an open-source napari plugin designed for processing and analyzing cryogenic serial pFIB/SEM images.
  • To provide tools for automated image registration, quality evaluation, and artifact mitigation in pFIB/SEM datasets.
  • To enhance the user-friendliness and accessibility of pFIB/SEM data processing.

Main Methods:

  • Development of Okapi-EM as a napari plugin leveraging Python programming.
  • Implementation of automated slice registration algorithms.
  • Inclusion of image quality metrics specific to pFIB/SEM imaging.
  • Development of methods for mitigating charging artifacts in SEM images.

Main Results:

  • Okapi-EM facilitates automated processing of cryogenic serial pFIB/SEM images.
  • The plugin enables accurate image registration and effective mitigation of charging artifacts.
  • It provides specific image quality metrics for pFIB/SEM data evaluation.
  • The napari framework ensures a user-friendly graphical interface and developer accessibility.

Conclusions:

  • Okapi-EM significantly improves the processing and analysis of cryogenic serial pFIB/SEM data.
  • The plugin enhances the precision of 3D reconstruction for biological samples.
  • Okapi-EM offers a user-friendly and accessible solution for researchers utilizing pFIB/SEM microscopy.