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Electron Microscopy

Segmentation and Analysis

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Interpreting electron microscopy images requires an experienced eye.  The Imaging Facility can provide expert assistance in assessing the quality of EM data, explain what the data shows (e.g. identify relevant organelles) and give guidance on data presentation.  For challenging applications, such as volumetric EM data segmentation and correlative imaging data registration, the Facility has dedicated software tools running on a powerful workstation.  Segmentation and analysis can be offered as a service, although the time-consuming nature of some workflows requires individuals to be trained to perform tasks independently.

 

Our Software:

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Amira (ThermoFisher)

  • 2D/3D visualisation for light and electron microscopy data

  • Allows measurement of shapes, sizes, and volumes

  • Links data from light microscopy, electron microscopy, and other imaging techniques into a single, aligned dataset.

  • Easy navigation through complex samples

  • Produces clear visuals and animations

  • Customisable workflows

  • Generates high-quality images and movies suitable for reports, presentations, or scientific publications

 

Microscopy Image Browser (MIB)

  • Free and accessible open-source tool

  • Community driven

  • Supports a wide range of microscopy image formats

  • 3D visualisation

  • Segmentation tools

  • Quantitative analysis

  • Correlative imaging support

  • Generates clear figures and 3D models suitable for reports, presentations, or publications.

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Napari with Empanada plugin

  • Free and open-source, community developed

  • Fast and interactive viewing

  • Empanada plugin uses deep learning to automatically detect and segment structures

  • Supports 2D and 3D data

  • Customisable with plugins

  • Ideal for correlative workflows, integrating and aligning images from different sources or imaging methods.

  • Simple interface for beginners, with advanced tools for expert users.

  • Produces visuals and outputs ready for presentations, reports, or publications.