flywatch

Code to analyse movies of flies.

For the time being principally based on Yoshi Aso’s (Janelia) behaviour rig as originally described in

Mushroom body output neurons encode valence and guide memory-based action selection in Drosophila. Aso Y, Sitaraman D, Ichinose T, Kaun KR, Vogt K, Belliart-Guerin G, Placais PY, Robie AA, Yamagata N, Schnaitmann C, Rowell WJ, Johnston RM, Ngo TT, Chen N, Korff W, Nitabach MN, Heberlein U, Preat T, Branson KM, Tanimoto H, Rubin GM.. eLIFE 2014 Dec 23;3:e04580. doi:10.7554/eLife.04580

Quick Start

For the impatient …

# install
if (!require("devtools")) install.packages("devtools")
devtools::install_github("jefferislab/flywatch")

# use
library(flywatch)

# run examples for plotting data from Yoshi Behaviour Rig
example("plot_ybr")
example("plot_smoothed_displacement")

# get overview help for package
?flywatch

# help for some interesting functions
?read_ybr_summary
?read_ybr_xy
?plot_ybr

Note: Windows users need Rtools to install with devtools.

Bugs, Feature Requests

If it doesn’t work or is missing a feature you can check if anyone else has complained and file an issue at github

Dolan analysis scripts

This repository also wraps a number of analysis scripts written by Mike Dolan for the paper originally preprinted as

Neurogenetic dissection of the Drosophila innate olfactory processing center Michael-John Dolan, Shahar Frechter, Alexander Shakeel Bates, Chuntao Dan, Paavo Huoviala, Ruairi J.V. Roberts, Philipp Schlegel, Serene Dhawan, Remy Tabano, Heather Dionne, Christina Christoforou, Kari Close, Ben Sutcliffe, Bianca Giuliani, Feng Li, Marta Costa, Gudrun Ihrke, Geoffrey Meissner, Davi Bock, Yoshinori Aso, Gerald Rubin, Gregory Jefferis bioRxiv 404277; doi: https://doi.org/10.1101/404277

most of these scripts don’t actually depend on the package itself, but can be found in the demo folder.