We have powerful workstations available with selected software programs (commercial or open source) for the post-processing and image analysis of microscope images. The workstations are available for scheduling in iLab. If you have specific post-processing needs regarding microscope data collected on our instruments, we will usually address these as part of the training on the instrument used to gather the data. Please feel free to ask us for assistance.
Depending on your needs (and our current expertise), we may be able to assist you in building an image analysis workflow. We have experience in thresholding and segmentation type analysis, but more elaborate workflows may be beyond our skillset or the capabilities of the software that we have available. Features that can often be quantitated include object counting, geometrical properties (length, area, perimeter, shape factors), and volumes can be estimated using stereological techniques. If we build a workflow, there may be a labor charge for our time.
Our thoughts on fluorescence quantitation - the software to quantitate fluorescence intensities is easy to find. Unfortunately microscopes are known to be subject to a number of physics, engineering, and optical variabilities that are difficult to control. This means that to correctly capture fluorescence data that can be accurately quantified, the user must be willing to be meticulous in their sample prep and to ensure that the instrument variables are carefully controlled for (as a start, see The 39 Steps: A Cautionary Tale of Quantitative 3-D Fluorescence Microscopy). Controlling the instrument to ensure accurate data is time consuming and non-trivial. It is our opinion that much of what passes as quantitative fluorescence in the published scientific literature is worthless.