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Disclaimer: these examples are mostly taken from my pre-Eikomagos career

Resolution estimation in optical nanoscopy

Nieuwenhuizen et al. [1] published a method to estimate the resolution in a super-resolution image. From the paper the resolution depends on localization uncertainty, density of single fluorescent labels and on the sample’s spatial structure. Their approach estimates the resolution directly from the final image or localisation coordinates.

The authors released their reference implementation in DIPimage. In addition, their group released a plugin for ImageJ/Fiji. However, the latter only implemented a stripped-down version of the methodology. In 2017 Eikomagos was commissioned to improve the plugin. In the end, we started from scratch so both 2D and 3D data sets could be supported using the JTransforms/JLargeArrays package to provide a Fourier transform implementation on large multi-dimensional arrays. The rewritten plugin fully implements:

  • The randomisation scheme as described in the paper
  • User interface with integrated graphs rather than popup windows
  • 2D and 3D FRC (Fourier Ring Correlation) resolution estimator
  • Spurious correlation correction and a UI pane to help you find the parameters for the correction
The implementation was based directly on the paper (requiring a thorough read) and testing against the reference DIPimage implementation. The plugin has not yet been released by the authors pending in-house testing in their group.


Recording of the plugin in action as it processes the data for figure 2a of the paper.

As we did not develop the methodology, this is a good place to focus on the implementation. imageJ is written in Java and we had no prior experience in Java. As the result shows, this was no obstacle. This example also shows that providing a user interface is very much in scope as well. As we have the scientific background to understand the methodology, we can “think along” and implement it according to your requirements.

[1] R.J.P. Nieuwenhuizen, K.A. Lidke, M. Bates, D. Leyton Puig, D. Grünwald, S. Stallinga, B. Rieger ; Measuring Image Resolution in Optical Nanoscopy ; Nature Methods, 2013, doi:10.1038/nmeth.2448