Measuring Nuclear/Cytoplasmic Intensity with CellProfiler

Detailed walk-through of a CellProfiler pipeline to quantify nuclear localization of a protein from microscope images. I discuss the pros and cons of using the whole cytoplasm versus the perinuclear ring region and the importance of log transforming the ratio.
Labels used here were Hoechst (DNA and nuclear segmentation) and anti-YAP/TAZ (subcellular localization and cell segmentation).

[@matthewrich2599]

This was excellent! Well explained and not too long a video. I hope you come out with more videos showcasing some of the other features of cell profiler.

[@JamMcG]

Hi Julia, Great walkthrough! You've helped me get my head round some of the major hurdles using cellprofiler! Keep it up!

[@williamrodriguez4423]

Not sure if this comment will reach you but I wanted to ask if you had any recommended cytoplasmic dyes that are nicely used to count cytoplasmic puncta in human cells using cell profiler. Any advice would be greatly appreciated thanks!

[@cellmorphojsero6054]

Wow, very late reply, but maybe it will be useful to you or someone else! I guess it depends what sort of structures you are interested in. In my experience, the CellTracker vital dyes have different localization patterns in different cell types.