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pub:neuroanatomy:frulhns:start [2014/01/21 23:45] – [Data] jefferis | si:frulhns:start [2014/01/26 15:56] – Page moved from pub:neuroanatomy:frulhns:start to si:frulhns:start jefferis | ||
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+ | Supplemental data to accompany: | ||
+ | [[http:// | ||
+ | Cell, Volume 155, Issue 7, 1610-1623, 19 December 2013 [[http:// | ||
+ | Johannes Kohl*, Aaron D. Ostrovsky*, Shahar Frechter, Gregory S.X.E. Jefferis | ||
+ | |||
+ | ====== Data ====== | ||
+ | The following data is available to accompany the publication | ||
+ | |||
+ | * Tabular data underlying the figures is available through a dedicated R package, [[https:// | ||
+ | * The vignette for this package completely recreates the Supplemental statistics table for the paper. | ||
+ | * The current version of the package requires the [[https:// | ||
+ | * Cached versions of the vignettes (frulhns v0.4.1) are available here: | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | * Traced Neurons | ||
+ | * before registration | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | * after registration to IS2 template brain | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | * 3D confocal image data (on a hard drive, on request to Greg) | ||
+ | ====== Electrophysiological Analysis ====== | ||
+ | Analysis and plotting of electrophysiological data initially acquired with Neuromatic/ | ||
+ | |||
+ | <code python> | ||
+ | # Start R | ||
+ | |||
+ | # install (one time only) | ||
+ | install.packages(" | ||
+ | install.packages(" | ||
+ | # download gphys package from Jefferis lab website to a temporary file | ||
+ | download.file(' | ||
+ | # install | ||
+ | install.packages(tf, | ||
+ | # clean up temp file | ||
+ | unlink(tf) | ||
+ | |||
+ | library(gphys) | ||
+ | # get introductory help on package | ||
+ | ?gphys | ||
+ | # get help on main plot function (including examples) | ||
+ | ? | ||
+ | </ | ||
+ | |||
+ | note that this download includes full source code for the functions in the package along with documentation and examples. | ||
+ | ====== Methods ====== | ||
+ | Detailed methods are included in the manuscript supplemental information. Further information on these topics is available here | ||
+ | * [[alex: | ||
+ | * [[pub: | ||
+ | * [[warping_manual: | ||
+ | * [[https:// |