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Developed in the Parker Lab

University of California, Irvine, Neurobiology & Behavior

About CellSpecks

- elementary calcium event detection
- video TIRFM datasets
- automatic channel detection
- text and Metamorph region export

Channel attribution and working in the field

I have been working hard on making sure that events are associated with the proper channel in CellSpecks. As this is the primary task and primary challenge, this can obviously take some time. While there are a few different approaches, I think I am generally making progress.

Code commenting

CellSpecks is being pushed forward toward a public release! I am currently working on cleaning up and commenting the code so that the other researchers in my lab can thumb through it and see what they think from a biological perspective. This is a bit of a challenge as the program consists of 50 classes averaging a few hundred lines of code a piece (up to several thousand in some cases).

Channel Chip Background Leveling and Interface Abstraction

Done with leveling the backgrounds on the channel chip! For the time being I'm going with a manual technique: specify the section you want to depict as uniform, I will make it uniform. While I was trying to avoid this manual interaction for the detection algorithm (it should be automatic, and you should be able to crop datasets without leaving the leading control), for the purpose of producing a visual reference I think it works for now.


Before the first public release of CellSpecks, I have been endeavoring to replace the current GUI with something that is more familiar to my collaborators. To that end I'm working on a general restructuring, separating the front and back ends and making them entirely independent. This adds a layer of abstraction that will allow me to work on each functional unit more independently, without having to remind myself of the inner workings of the other units.

Polishing figures

While Dr. Demuro is working on his own manuscripts and research, I have been attempting to code for the generation of a production quality channel chip. Thus far I have successfully taken the ArrayList of detected channels and sorted the channels by open probability. I then array them in the proper channel chip orientation and voila, a channel chip is born. I haven't touched Look Up Tables yet, as ImageJ does those so well and they would take a while to code (especially if you wanted to do your own custom ones or a have a variety from which to choose).

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.

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