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

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.