nat.as-package: Analyse 3D biological image data especially neurons

In jefferis/nat.as: NAT: Wrapper for informal neuroanatomy AnalysisSuite codebase

Description

This packages provides a thin wrapper for the extensive neuroanatomical image analysis functionality in the AnalysisSuite package that has been developed and used in a number of publications from my lab (see references for key examples).

Details

Before you can use the main functionality of this package, you must install the https://github.com/jefferis/AnalysisSuite codebase using install_analysis_suite. The package README on github contains details:

https://github.com/jefferis/nat.as

In future you can simply use library(nat.as) or require(nat.as) to load the full AnalysisSuite codebase. Note that the functions will loaded into the nat.as namespace and then exported to avoid polluting the global namespace. If you are hacking AnalysisSuite, you can use reload_analysis_suite() to reload code.

Key functions within AnalysisSuite that you will want to look at include:

• read.neuron

• write.neuron

• plot.neuron

• plot3d.neuron Objects of class

• neuron

• neuronlist

References

[1] Grosjean Y., Rytz R., Farine J.P., Abuin L., Cortot J., Jefferis G.S.X.E., and Benton R. (2011). An olfactory receptor for food-derived odours promotes male courtship in Drosophila. Nature 478 (7368), 236–40. doi:10.1038/nature10428

[2] Cachero S., Ostrovsky A.D., Yu J.Y., Dickson B.J., and Jefferis G.S.X.E. (2010). Sexual dimorphism in the fly brain. Curr Biol 20 (18), 1589–601. doi:10.1016/j.cub.2010.07.045

[3] Jefferis G.S.X.E., Potter C.J., Chan A.M., Marin E.C., Rohlfing T., Maurer C.R.J., and Luo L. (2007). Comprehensive maps of Drosophila higher olfactory centers: spatially segregated fruit and pheromone representation. Cell 128 (6), 1187–1203. doi:10.1016/j.cell.2007.01.040

See Also

install_analysis_suite, reload_analysis_suite and rgl-package which is used for visualisation.

jefferis/nat.as documentation built on May 19, 2019, 3:06 a.m.