Commoditizing population calcium imaging analysis



More open source software to check out.

Two-Photon Processor and SeNeCA – A freely available software package to process data from two-photon calcium imaging at speeds down to several ms per frame.
Jakub Tomek, Ondrej Novak, and Josef Syka
TJ Neurophysiol published 10 April 2013, 10.1152/jn.00087.2013

It’s notable in that it is an “all-in-one” package that’s freely available.

The image processing to detect cells and draw ROIs seems to work pretty good, even with poor S:N. I’d like to see it operate on GCaMP images, since those are more challenging in some ways. Cells labeled with Oregon Green BAPTA-1 tend to exhibit spherical patterns of somatic fluorescence, but GCaMP, when it’s working well, does not brightly label the nucleus, so the shape of the ideal ROI is quite different. Plus, it’s nice to pick up dendrites and other features, not just somata.

See also, Vogelstein’s code for inferring action potentials in calcium imaging data.


Hat tip to Christian Wilms
EDIT: The code became available shortly after this post.

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