OpenScope Software v1.0

School has a way of keeping you busy. Very busy. But don’t worry; I’ve been working hard at building awesome stuff! In particular, I’m still making progress on my open microscope design. The fluorescence works, but I’m still in the stages of trying to optimize it (and seeing if I can reduce the cost of the final design). However, I’ll probably make another post soon with some proof of concept images and a general outline of how it works. While the physical microscope is still in the works, I managed to make some serious progress in writing software for it!

I’ve always been surprised at how expensive professional microscope imaging software is, and how *repetitive* the tasks are for it. It’s almost like photoshop… you just need a ‘count number of particles’ button, a ‘calculate intensity’ button, ‘calculate area’, and so on… So I figured I’d try my hand at writing some basic image analysis software and see where it takes me.

The result is ‘OpenScope Software’, which I intend to release as a software package to go with the hardware for OpenScope. Right now there’s two tasks I want to be able to do with fluorescence microscopy:
-Calculate the intensity/brightness of a selected region of interest
-Track that region of interest across a sequence of images so I can track the fluorescence vs. another parameter (such as optical sectioning, introduction of a drug, etc.).

OpenScope software uses Python Imaging Library and TKinter to do just that. It creates a RegionOfInterest object that track a region of interest, can draw a box around it, and computes values using the pixel data (including when the pixel data changes). It also has a Sequence object that handles loading a series of images labelled numerically (such as image01.jpg, image02.jpg, image03.jpg… until the last image) so that you can perform image analysis on optical sections or videos of fluorescence microscopy.

Example of OpenScope Software v1.0

The code is available on github here:; the README file includes the instuctions for the few features it has, along with a test image.

Coming Soon: Some more software features and a physical fluorescence microscope to go with it!


~ by asymptoticdesign on 29 March, 2012.

One Response to “OpenScope Software v1.0”

  1. This is great! My wife is doing neuroscience research and we were just talking about automating the tracking of various marked regions over a series of images since something like that is very difficult for an avg human depending on the density.

    I have some basic python skills and very basic understanding of neuroscience and would be happy to help out if have outstanding features you’re trying to implement.

    I’d also be very interested in your openscope hardware. You should look into starting a Kickstarter project if monetary resources are an issue.

    Great work, very much appreciated. Keep it up!

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