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README.md

README for the Weir et al. 2017 paper data

This repository contains the following:

  • Sample scripts for segmentation of peroxisomes and mitochondria followed by fluorescence intensity measurement using pyto_segmenter (see sample_segmentation folder)
  • Post-segmentation and fluorescence intensity measurement data, in csv format, for each quantitative microscopy experiment
  • R scripts for generation of quantitative microscopy

Two other repositories are critical for complete re-production of the analyses in this paper:

  • pyto_segmenter package (above)
  • Dryad repository of raw microscopy data

Before trying to re-capitulate segmentation using the scripts in sample_segmentation, be sure to read the readme within that folder.

The R scripts contained in this repository require the following packages to be installed:

  • readr
  • plyr
  • dplyr
  • ggplot2
  • gridExtra
  • Cairo
  • minpack.lm

See pyto_segmenter for the list of python dependencies.

Last updated 9.5.17

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Scripts for analysis and figure generation in Weir et al. 2017

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