Micron Image Analysis Software



SIMcheck is a suite of ImageJ plugins enabling users to identify and avoid common problems with 3D-Structured Illumination Microscopy (3D-SIM) data, and assess resolution and data quality through objective control parameters. Additionally, SIMcheck provides advanced calibration tools and utilities for common image processing tasks. This open-source software is applicable to all commercial and custom platforms, and helps promote routine application of super-resolution SIM imaging in cell biology. 

For further information read the publication.

To get started please refer to the SIMcheck manual 

For the open source code download from GitHub 

Developed by the Micron Team, led by Graeme Ball, Ian Dobbie & Lothar Schermelleh



Advanced fluorescence imaging methods require careful matching of excitation sources, dichroics, emission filters, detectors, and dyes to operate at their best. This complex task is often left to guesswork, preventing optimal dye:filter combinations, particularly for multicolour applications. To overcome this challenge we developed SPEKcheck, a web application to visualise the efficiency of the light path in a fluorescence microscope. The software reports values for the excitation efficiency of a dye, the collection efficiency of the emitted fluorescence, and a "brightness" score, allowing easy comparison between different fluorescent labels. It also displays a spectral plot of various elements in the configuration, enabling users to readily spot potential problems such as low efficiency excitation, emission, or high bleedthrough. It serves as an aid to exploring the performance of different dyes and filter sets. 

You can use the tool here

For help please refer to the manual

For more information on SPEKcheck click here.

Developed by the Micron Team, led by David Pinto, Mick Phillips and Ian Dobbie.

Particle Stats


The study of dynamic cellular processes in living cells is central to biology and is particularly powerful when the motility characteristics of individual objects within cells can be determined and analysed statistically. However, commercial programs only offer a very limited range of inflexible analysis modules and there are currently no open source programs for extensive analysis of particle motility. ParticleStats is, a web server and open source programs, which input the X,Y co-ordinate positions of objects in time, and outputs novel analyses, graphical plots and statistics for motile objects. For more information click here.

Developed by Russell Hamilton