Has anyone used the ‘Squassh’ plug-in for imageJ in the paper “Segmentation and quantification of sub cellular structures in fluorescence microscopy images using Squassh” by Rizk et al. published in Nature Protocols in 2014? I am trying to understand the differences between Squassh and the CellProfiler and whether it would be beneficial to use them in combination.
I’ve not used Squassh before, so hopefully someone here has and can give you some on-the-ground feedback, but from looking at the paper (which is quite cool!) my thoughts are:
CellProfiler’s strengths are a) adaptability, b) number/types of measurements, and c) scalability. Squassh allows you to do deconvolution (which CP does not at the moment) and automates a lot of the most common steps up to and including the data analysis, but at the expense of flexibility - it looks like it’s basically designed to use two channels only and doesn’t seem to offer as many measurement parameters as CP does.
I could definitely image a workflow where if you had a tricky segmentation but wanted to measure lots of features or many channels you could segment and export masks in Squassh and then do measurements in multiple channels in CP, but whether either or a combination of the two is the best for your particular question seems highly dependent on the details of your experiment.