How do I check for image processing artifact?


I had recently started using Cellprofiler to process my Fura fluorescent images, and I noticed sub-cellular regions with varying intensities. How should I check whether the patterns I saw came from biological property or if it’s a result of mathematical or optical artifacts, and what does it mean?



Typically speaking, if the effect you seeing occurs across multiple images for a given experimental series (i.e, images acquired with the same imager and acquisition settings, etc), regardless of treatment or control conditions, then you may be dealing with a systemic aberration that may be hardware-related.

If the effect varies depending on spatial position of the individual sample, e.g., wells in the same location on a plate are affected the same way, then you may be dealing with the sample preparation problem.

On the other hand, if this effect you are seeing varies depending on the treatment, etc, then it may be biologically-related and biologically relevant. But it’s difficult to assess without actually seeing a sample image.