Semi-automated

The macro generates orthogonal projections from bead images along the lateral and axial dimensions which are displayed using a customized look-up-table to color code intensities. A Gaussian curve is fit to the intensity profile of a fluorescent bead image and full-with-at-half-maximum (FWHM) values are extracted, and listed next to theoretical values for comparison. 

This plugin allows measuring relevant parameters which helps testing, following and comparing microscopes performances. This is achieved by extracting four indicators out of standardized images, acquired from standardized samples: the estimation of the detector sensitivity, the evaluation of the field illumination homogeneity, the system resolution, and finally the characterization of its spectral registration.

Spimagine is a python package to interactively visualize and process time lapsed volumetric data as generated with modern light sheet microscopes (hence the Spim part). The package provides a generic 3D+t data viewer and makes use of GPU acceleration via OpenCL. If provides further an image processor interface for the GPU accelerated denoising and deconvolution methods of gputools.

It is only for display (no analysis). The only drawback: it does not handle multichannel time lapse 3D data (only one channel at a time).