Pipeline of bacteria analysis?

Hi, I am wondering if I could get some help on analyzing bacteria information by cellprofiler, I have attached a TIFF file as an example. Briefly, I have two different bacteria cells in the confined chamber (red or green). What I want to analyze are: 1) how many cells (cell number) of each kind (red and green) in this chamber 2) some of the bacteria have two colors (both red and green), what is the percent of two-color cells in the whole chamber 3) if I have a time-lapse data, how I could align all the frames and analyze all the image in the same pipeline. Also, I want to make a circular mask to shape the chamber first before the analysis. Thanks a lot on any sort of help :smiley: ~


I created a pipeline to get you started (attached). There are notes I wrote at the top of some of the modules to explain my thoughts.

  • In Metadata, you have to click BOTH “Update” buttons (one is labeled “Update metadata”
  • The channels are labeled Ch0 and Ch1. Red and green are just pseudo-colors – feel free to rename in NamesAndTypes.
  • There are two IdentifyPrimaryObjects modules, one for each channel, that likely need to be tweaked. That’s up to you!
  • Further notes are in the modules themselves

As for your question about time-lapse, check out (in CellProfiler app) Help menu > Creating a Project > Loading Image Stacks and Movies. This gets you started loading them at least. Each frame will be analyzed independently. If you want to track the movement of cells, check out the TrackObjects module.

Hope that helps!
DL_Attempt1.cppipe (11.3 KB)