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Developed in the Parker Lab

University of California, Irvine, Neurobiology & Behavior

CellSpecks Development Update November 22, 2009

CellSpecks is a project I have been working on for the last two years (since fall 2007) as a project in the lab of Dr. Ian Parker at the University of California, Irvine. I have been the sole developer on the resulting software, and as such there is still a lot to do.

Details below the fold...

A significant amount of work has thus far gone into the project (8 quarters, 10 weeks a quarter, 15 hours a week = 1200 hours) but development spanned my initial experimentation with Java. As with any project, if you try to maintain a significant amount of code over a significant amount of time you are stuck with some of the decisions you made in the past, even if they were made in your first quarter taking Computer Science classes. I shall continue to work on polish, functionality, and QA, and hopefully there will be a public release sometime in the near future. I have yet to determine what license the software will be released under as it is up to the University of California.

The goal of the project is to provide a tool for automatically detecting elementary calcium events in video datasets from TIRFM. To this end I have created a number of libraries, a graphical user interface, and an automatic detection algorithm capable of detecting the location of channels with a high degree of accuracy. This increases the frequency of detection of small or infrequently opening channels versus manual analysis while decreasing the necessary duration. Technical details to follow.

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