New project - Microscopy Real Time Image Processing

Dear Igorians,

I have been contemplating the idea of starting a new project and I seek your advice, comments, suggestions etc.
Only with the start of this year I have taken more seriously the idea of programming, and I have only experience in doing so with Igor.

I have developed a series of scripts that allow me to assess dynamic behavior in video microscopy and I have done so, first by manipulating images with ImageJ, from which I obtain a time-trace, which I then import into Igor for further quantitative and statistical characterization of events therein.

However, I have been wondering about implementing this on the fly. From the hardware side I should be safe: currently I am obtaining videos with 512x512 pixels/frame with 7.5 FPS and I can ramp this up to 30FPS using a Andor iXon camera (eventually to be improved to a solution with 1MP pixel camera working at ~100 FPS) and this is coupled to high spec computer (64 GB RAM, high end i7 processor, equipped with Samsung EvoPro SSD's with PCIe interface, etc.)

I was hoping that maybe some of you with more experience either in image analysis or data acquisition would be able to make some comments and share your experience.

I see two possibilities: (1) grab data with Mikromanager and implement real-time analysis in ImageJ, or (2) do everything with Igor. The second solution has the obvious advantage that I can use the code I have already written, but there may be reasons to go with first solution.

Please let me know your thoughts on this.


Hello R.,

I don't think that you will find too many people who would love a design that requires using two different applications.

In order to do real-time analysis you need to acquire the images directly into Igor. To do so you need to start with an XOP that supports the camera or acquisition system. Writing an XOP is not very difficult if you are a competent c/c++ programmer and have access to a decent sdk from the camera manufacturer. If you are not a good c/c++ programmer the scope of the project is probably not ideally suited for you.

WaveMetrics, Inc.