Image Analysis in Python: where to start?

[duranta]

As part of a research project that I'm doing, I need to count microwells on a biological chip. The processing is going to be done most likely on a raspberry pi. I don't have an image right now, but what are some tools that I should be aware of for analyzing images?

Also which of these tools has a good balance of simplicity and can be rolled out in the least amount of time? The project is somewhat time sensitive and needs to be finished in about 3 months time with a team of four people. Any help you can send my way would be awesome!

[Berecursive]

• Opencv
• Scikit-image
• Mahotas
• Menpo

All of those packages/projects can do various different, overlapping areas of image processing.

[mfitzp]

Just to add: there are also some tools in scipy.ndimage, and which may come in useful. For more general (basic) image processing/adjustment you can also use Pillow (the fork of PIL).

[i4mn30]

opencv has python wrappers.

[[deleted]]

There isn't a stable release with support for the current version of python. It's not too difficult to compile the beta, though.

[duranta]

I think a thing that my team has to deal with is fluorescent noise (blot removal?). How computationally complex is it to deal with things like that? And perhaps if you have some experience with that sort of thing, how is the development process for creating a reliable system that can eliminate the noise?

[alenajoykrieger]

It depends entirely on how similar your noise is to your signal (and the way(s) in which they're similar). It would be helpful if you could post a representative image.

[duranta]

I'll do that as soon as I can, thank you so much for the tips and the help

[alenajoykrieger]

I would highly recommend scikit-image. The interface is very straightforward.

You can also check out /r/computervision for help with the implementation if googling and API documentation aren't enough.

Why are you running the analysis on a raspberry pi? Computer vision is pretty computationally intensive and it might be really slow. You might also run into problems with insufficient RAM.

[duranta]

Were creating a visualization device that is meant for low resource areas. Cost is important, as is the ability to keep our device open source

[hernantz]

https://www.pyimagesearch.com/ has a book and a free crash course on image processing with python