[Coral-List] Re: Image-analysis software for counting (Matthew Johnston)

zoerscott8 at gmail.com zoerscott8 at gmail.com
Fri Jun 12 12:42:50 EDT 2015

 Hi Becca,

Though I don't have much experience with image-analysis, a colleague of mine uses image-J for counting bacterial cells in her cultures. She recommends using the multipoint tool, which would be a way to manually count the bore holes. As you click on each bore hole, the program keeps tally and will give you a total at the final point. If you’re interested in automating the counting, she says that it is a bit more challenging to set the program up to recognize your items, especially if they are overlapping. You can get the software at http://imagej.nih.gov/ij/, and here is a paper that talks about using the two types of counting, hope it helps!



Zoë Scott
M.S. Candidate I Department of Biology
California State University, Northridge
Eco-Evo Lab
zoe.scott.923 at my.csun.edu


Dear Coral list,


> I am analysing images of long term monitoring quadrat photos for

> evidence of barnacles on a species of *Orbicella.* Any suggestions for

> image-analysis software that allows me to place a point on each of the

> bore holes (more than 100 on some colonies) and count the total points?


> Thanks!


> Becca Maher

> Ecology and Evolutionary Biology

> Rice University '16

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