Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. It's 100% free, no registration required.

Sign up
Here's how it works:
  1. Anybody can ask a question
  2. Anybody can answer
  3. The best answers are voted up and rise to the top

I am looking to start doing some work tracking the size and growth of individual bacterial cells in the microscope. In order to analyze the images I need software that can segment the cells, accurately determine their shape, and track cell lineages on a 'movie' of images collected from one experiment. Given the constraints of my microscope setup, the easiest thing for me to do is to use a strain of bacteria constitutively expressing GFP and segment the cells based on fluorescent intensity. This is functionally equivalent to segmented phase-contrast images of wild-type cells, i.e. I'm not that interested in changes in fluorescence or using fluorescence as a gene expression reporter, though my needs may head in that direction.

I don't want to reinvent the wheel (and I think that it's better if the community consolidates around a few programs that everyone uses so that experiments can be more comparable), so I'm looking for a previously published package that is robust and easy to use. Flexibility at measuring fluorescent tracking is nice, but at this stage is not crucial. The two packages that I have seen are Schnitzcells from the Elowitz lab at CalTech and Microbetracker from the Emonet and Jacobs-Wagner groups at Yale. Unfortunately they were released at the same time and don't provide a good comparison of the pros/cons of each tool.

Finally, my question is

What are your recommendations for an image analysis suite (from the two packages above or another package you have used)?

Let me know if I can make my criteria more clear or anything else. Thanks!

share|improve this question
Although I haven't done live image tracking and analysis myself but I know the main method that people use is through Matlab, which means programming/coding so you would have to find someone to help you with some coding if you haven't worked with it before. Otherwise I suggest looking at fiji Image-J since it has a wide variety of open source plug-ins. I personally use image-J very very frequently and I'm very happy with it. – Bez May 10 '14 at 16:20

Your Answer


By posting your answer, you agree to the privacy policy and terms of service.

Browse other questions tagged or ask your own question.