Software Development at Micron

SIMcheck

Three-dimensional structured illumination microscopy (3D-SIM) is a versatile and accessible method for super-resolution fluorescence imaging, but generating high-quality data is challenging, particularly for non-specialist users. We present SIMcheck, a suite of ImageJ plugins enabling users to identify and avoid common problems with 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 will promote routine application of super-resolution SIM imaging in cell biology. To download v1.0 click here

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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. Here, we describe ParticleStats (www.ParticleStats.com), 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. 



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Cockpit

Cockpit is a revolutionary new Python-based biologist-friendly software interface for controlling and using bespoke microscopes built by physicists and engineers to tackle challenging biological questions. At the heart of the approach is the use of a touch screen containing a “google-earth” style map of the entire specimen held in graphics card memory, allowing near-instant navigation of the landscape using an X-box controller. The basic principle behind our software is to provide simple and efficient workflows for use of the most advanced microscopes by biologists and includes an inexpensive but flexible master timing control device. At the same time, the complexity of controlling some of the most advanced and complex optical devices is hidden. Driving all the complex hardware devices is “Microscope”, a python based abstracted set of drivers with a unified grammar, to which suitably qualified hardware engineers can add devices according to specific “recipes”. Microscope already controls many CCD and SCMOS cameras from the most popular manufacturers, high end piezo slip stick stages, lasers, adaptive optics mirrors, spatial light modulators and various optomechanical devices in common use in home built advanced microscope hardware. This tool is still under development and not yet available to users.

SPEKcheck

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.