Allen Cell Discussion Forum

Why python, not imageJ?

I am a relatively new user of automated image analysis methods. I am developing automated counting and tracing methods for multi well plates for primary neuronal cultures - using both standard and confocal microscopy. This has been challenging as we are producing 100s of GBs of data - especially since, I’m in a predominantly ephys lab. I have managed to achieve quite a lot using imageJ - and find it useful. I work with R and imageJ - being pretty competent (for a biologist) in both. I have tried to get an answer to this question in looking in all the obvious forums etc. Why do you use python to do your image analysis - I know the packages etc. are expanding in utility? Is there a place to get a better understanding of the imageJ vs python based image analysis question? Or is that fact that I am asking this question just a sign that I am still relatively green in this domain - and will figure it out myself with more experience? Thanks!

This is indeed a very good question. There are a lot questions online, like which one should I learn, language A and language B? Every tool/language gains its popularity for a reason. The tool/language that can solve your problem is the right one.

Meanwhile, there are some other considerations:

(1) Using tool A does not mean you cannot use tool B. For example, I use both python and ImageJ , simply according to the job to be done.

(2) I have admit ImageJ is very convenient in many cases. But, I find quite a lot scenarios that Python provide better help. To name a few, most deep learning stuffs are implemented in python. Also, python provides an easier way to building a workflow integrating image processing, data analysis, visualization, etc…

So, in short, it is okay to use any language, as long as getting your jobs done. But, mastering more languages/tools is always helpful, considering the power of python.

Hope this helps.

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Thank you for the answer - informative and useful!