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I did a test which involved growing e. coli on a petri dish. I did not dilute the sample, and this resulted in growing hundreds of small, overlapping colonies. However, they still can be counted, but it has been tedious work. Does anyone have tricks for counting small colonies? Also, I've read people will just write >300 if their colony count is too large. Is this data sufficient? I need to compare the colony count for several petri dishes and they all have quite a lot. If i just write ">300" for 80% of my data, it won't be a very good comparison. Can anyone help me out here?

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  • $\begingroup$ I had once learned of a method where you can observe through a microscope and do a calculation. However, I can't remember the exact procedure over the top of my head. Do a google. $\endgroup$ – The Last Word Nov 14 '18 at 0:57
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    $\begingroup$ Read this on why people report >300. It’s acceotable depending on what you are doing. If you need an actual count, you need to dilute the original culture. $\endgroup$ – canadianer Nov 14 '18 at 18:41
  • $\begingroup$ I'm seeing an opportunity for some image analysis here. Sounds like you could tweak some basic segmentation methods to at least approximate the number of seeds on your plate, but you'll need to work yourself into FIJI (fiji.sc) or a similar image analysis software. Might be able to get help at the forum at forum.image.sc/tags/fiji $\endgroup$ – Armatus Nov 15 '18 at 11:01
  • $\begingroup$ Actually, Cell Profiler (cellprofiler.org) might have out-of-the box functions that could count your dots, but the image format might need some adjusting. $\endgroup$ – Armatus Nov 15 '18 at 11:04
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Divide the plate into equal sectors. Count one sector as accurately as you can then multiply that number by the number of sectors. This assumes the colonies are roughly equally distributed.

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