Take a look at this fantastic preprint by Senft et al. on A biologist’s guide to the field of quantitative bioimaging!
The authors guide us through the different ins and outs in quantitative bioimaging. starting with sample prep up until image data acquisition, analysis, and interpretation.

A quick summary:
–       Samples: cells, tissues, animal ex vivo, intravital imaging
–       Choice: application dependent
–       Sample prep: optimization is a prerequisite for quality images!
–       Guidelines for image acquisition
–       Software: application-dependent, but suggesting: ImageJ, CellProfiler, QuPath, Nepari.
–       Data management & storage: also application-dependent, but suggesting OTERO.
–       Prevalent image analysis methods. Most companies are focused on trending towards less qualitative, more quantitative data –> quantitative bioimaging.
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Highly-recommended, check it out here!