Detect Spots

I need to detect spots in my cells. There are different “Detect spots” modules but I didn’t find much info on them in the manual. What is the difference between the different modules and what kind of values make sense to put in?
The spots I want to detect are very small and have quite low contrast compared to the background. Sometimes they are a little bit out of focus as well. Any input and shared experiences will help. Thank you so much in advance!
Simone Graber

Hi Simone,

I would recommend checking out our Examples page and download the speckle counting pipeline, if you haven’t already. Keep in mind that additional tweaking of the pipeline is probably needed, so it may not work on your images immediately. The module is annotated so you can get a sense of the thought-process as well as what would need to be changed for your assay.

Based on the speckle counting pipeline, and from your description of your images, it seems that you will probably need to pay the most attention to the filter size setting in EnhanceOrSupresssFeatures, as well as the lower threshold bound in IdentifyPrimaryObjects in order to make sure you don’t get too many false positives.