Shared software

Much of our lab's share software is available at our Github site. 

ImageJ / Fiji Plugins

Parallel-enabled Extended Depth of Field: 

We modifed the Extended Depth of Field plugin created by the Unser Lab so that the output image is the original image name plus the suffx "_EDF". We have also fixed a bug where the topography map was shown when the checkbox was selected not to show it. This change was made to allow multi-core computeres to split multi-channel Z-stacks into separate channels and to process each channel in parallel. While likely not as fast as it might be if the plugin were multi-threaded, this approach provides several-fold increases in speed. This is especially true of hyperthreading processors. We have created a batch processing macro to accompany this versoin of the plugin. Our Mavenized plugin version is available at Github along with the ImageJ macro. 

ImageJ / Fiji Macros

Recursive ImageJ Particle Analyzer (RIPA):

This macro runs the ImageJ particle analyzer over a series of user defined thresholds and collects ROIs meeting user specified shape and size criteria. The greately increases the users ability to semi-automatically generate ROIs around a set of objects despite variantions in object or local background intensity. This was described thoroughly in our AJP paper. Current versions of the code are available at GitHub. We have also created a shell macro to run this macro for batch processing of all images in a folder. Please contact for more information

Multi-Image Nearest Neighbour Colocalization (MINER): 

Also descrived in our AJP paper, this macro performs a nearest neighbour search in 2-3 channel images. A "reference" channel is assumed to have a matching set of ROIs and up to 2 "nearest neighbour" channel containing some kind of blobs or puncta will be analyzed with or without predifined ROIs. This macro pairs nicely with a bottle of Chianti and our RIPA macro. Current versions are available at GitHub. Notably, this maco is written for 2D analyzes. It performs a measure of the full-width half-max of all puncta, and reports the distance between the centers of each pair of reference and nearest neighbour puncta. Centres are defined as eith the geometric centre, the intensity weighted center of mass or the locus of a bi-axial gaussian fit. This method is able to detect differences in the distances between fluorescent puncta in multiple channels well below the difraction limit of light.